title: "Annotate and analyze nucleotide and amino acid sequences using biopython"
author: "Bhagirathi Dash"
date: "December 1, 2018"
output: html_documentimport sys
sys.stdout.write("Hello from Python %s\n" % (sys.version,))Hello from Python 3.5.6 |Anaconda, Inc.| (default, Aug 26 2018, 16:05:27) [MSC v.1900 64 bit (AMD64)]Affy, Align , AlignIO , Alphabet, Application, Blast,
CAPS, Cluster, Compass, Crystal ,
Data ,
Emboss, Entrez, ExPASy ,
FSSP ,
GA, GenBank, Geo, Graphics,
HMM ,
KDTree , KEGG ,
Medline , NMR ,
NeuralNetwork , Nexus ,
PDB, Pathway, Phylo , PopGen,
Restriction ,
SCOP, SVDSuperimposer, SearchIO, SeqIO, SeqUtils, Sequencing, Statistics, SubsMat, SwissProt,
TogoWS ,
UniGene , UniProt ,
Wise
import Bioprint(Bio.__version__)1.72help(Bio.Align)help(Bio.AlignIO)help(Bio.Alphabet)help(Bio.Blast)help(Bio.Entrez)help(Bio.GenBank)help(Bio.Seq)help(Bio.SeqIO)help(Bio.SeqRecord)help(Bio.Sequencing)help(Bio.SwissProt)from Bio import Blasthelp(Blast)Help on package Bio.Blast in Bio:
NAME
Bio.Blast - Code for dealing with BLAST programs and output.
PACKAGE CONTENTS
Applications
NCBIStandalone
NCBIWWW
NCBIXML
ParseBlastTable
Record
FILE
c:\users\bhagi\anaconda3\lib\site-packages\bio\blast\__init__.pyfrom Bio.Blast import NCBIWWWhelp(NCBIWWW.qblast)Help on function qblast in module Bio.Blast.NCBIWWW:
qblast(program, database, sequence, url_base='https://blast.ncbi.nlm.nih.gov/Blast.cgi', auto_format=None, composition_based_statistics=None, db_genetic_code=None, endpoints=None, entrez_query='(none)', expect=10.0, filter=None, gapcosts=None, genetic_code=None, hitlist_size=50, i_thresh=None, layout=None, lcase_mask=None, matrix_name=None, nucl_penalty=None, nucl_reward=None, other_advanced=None, perc_ident=None, phi_pattern=None, query_file=None, query_believe_defline=None, query_from=None, query_to=None, searchsp_eff=None, service=None, threshold=None, ungapped_alignment=None, word_size=None, alignments=500, alignment_view=None, descriptions=500, entrez_links_new_window=None, expect_low=None, expect_high=None, format_entrez_query=None, format_object=None, format_type='XML', ncbi_gi=None, results_file=None, show_overview=None, megablast=None, template_type=None, template_length=None)
BLAST search using NCBI's QBLAST server or a cloud service provider.
Supports all parameters of the qblast API for Put and Get.
Please note that BLAST on the cloud supports the NCBI-BLAST Common
URL API (http://ncbi.github.io/blast-cloud/dev/api.html). To
use this feature, please set url_base to
'http://host.my.cloud.service.provider.com/cgi-bin/blast.cgi' and
format_object='Alignment'. For more details, please see
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast
Some useful parameters:
- program blastn, blastp, blastx, tblastn, or tblastx (lower case)
- database Which database to search against (e.g. "nr").
- sequence The sequence to search.
- ncbi_gi TRUE/FALSE whether to give 'gi' identifier.
- descriptions Number of descriptions to show. Def 500.
- alignments Number of alignments to show. Def 500.
- expect An expect value cutoff. Def 10.0.
- matrix_name Specify an alt. matrix (PAM30, PAM70, BLOSUM80, BLOSUM45).
- filter "none" turns off filtering. Default no filtering
- format_type "HTML", "Text", "ASN.1", or "XML". Def. "XML".
- entrez_query Entrez query to limit Blast search
- hitlist_size Number of hits to return. Default 50
- megablast TRUE/FALSE whether to use MEga BLAST algorithm (blastn only)
- service plain, psi, phi, rpsblast, megablast (lower case)
This function does no checking of the validity of the parameters
and passes the values to the server as is. More help is available at:
https://ncbi.github.io/blast-cloud/dev/api.htmlseq1 = open('seq1.fasta').read()seq1'>seq1\nCATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC\n\n\n\n'seq1_handle = NCBIWWW.qblast("blastn", "nt", seq1)from Bio.Blast import NCBIXMLseq1_blast_record = NCBIXML.read(seq1_handle)len(seq1_blast_record.alignments)50E_value_thresh = 0.01for alignment in seq1_blast_record.alignments:
for hsp in alignment.hsps:
if hsp.expect < E_value_thresh:
print('*****alignment*****')
print('sequence:', alignment.title)
print('length:', alignment.length)
print('e-value:', hsp.expect)
print(hsp.query)
print(hsp.match)
print(hsp.sbjct)*****alignment*****
sequence: gi|1500174811|gb|MK044561.1| Zaire ebolavirus isolate ZEBOV/Human/DRC/2014/BOE_036, partial genome
length: 18898
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1500174801|gb|MK044560.1| Zaire ebolavirus isolate ZEBOV/Human/DRC/2014/BOE_023, partial genome
length: 18870
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1500174791|gb|MK044559.1| Zaire ebolavirus isolate ZEBOV/Human/DRC/2014/BOE_011, partial genome
length: 18896
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1500174781|gb|MK044558.1| Zaire ebolavirus isolate ZEBOV/Human/DRC/2014/BOE-070, partial genome
length: 18784
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1487704041|gb|MH898466.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK012, partial genome
length: 18887
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301462|gb|MH733491.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK137, complete genome
length: 18939
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301452|gb|MH733490.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK091, complete genome
length: 18932
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301442|gb|MH733489.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK055, complete genome
length: 18913
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301422|gb|MH733487.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK046, complete genome
length: 18919
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301412|gb|MH733486.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK045, complete genome
length: 18914
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301402|gb|MH733485.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK039, complete genome
length: 18940
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301392|gb|MH733484.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK037, complete genome
length: 18905
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301382|gb|MH733483.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK031, complete genome
length: 18944
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301372|gb|MH733482.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK026, complete genome
length: 18944
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301362|gb|MH733481.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK025, complete genome
length: 18939
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301352|gb|MH733480.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK019, complete genome
length: 18938
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301342|gb|MH733479.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK016, complete genome
length: 18944
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301332|gb|MH733478.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK011, complete genome
length: 18941
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1453301322|gb|MH733477.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/COD/2018/Tumba-BIK009, complete genome
length: 18894
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1436008541|gb|MH613311.1| Zaire ebolavirus isolate H.sapiens-wt/COD/2017/Muyembe.1, complete genome
length: 18899
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1431829175|gb|MH464889.1| Vector pEBO_BDBV-GP, complete sequence
length: 21172
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1431829165|gb|MH464888.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-rec/COD/1976/Yambuku-Mayinga-eGFP-BDBV_GP, complete genome
length: 18962
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1425140432|gb|MH481611.2| Zaire ebolavirus strain Ebola_virus/DRC/Likati/Human/2017/1, complete genome
length: 18898
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1390208419|gb|MH121168.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/Zaire/1976/Mayinga-R3816, complete genome
length: 18958
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1390208399|gb|MH121166.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1976/Yambuku-Mayinga, complete genome
length: 18957
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1390208389|gb|MH121165.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621, complete genome
length: 18959
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1390208379|gb|MH121164.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621, complete genome
length: 18958
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1129866795|gb|KY425656.1| Zaire ebolavirus isolate IRF0164, partial genome
length: 18899
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1129866765|gb|KY425653.1| Zaire ebolavirus isolate IRF0120, partial genome
length: 18894
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1129866755|gb|KY425652.1| Zaire ebolavirus isolate IRF0150, partial genome
length: 18890
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1129866739|gb|KY425649.1| Zaire ebolavirus isolate IRF0206, partial genome
length: 18907
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1129866719|gb|KY425647.1| Zaire ebolavirus isolate IRF0147, partial genome
length: 18902
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1129866668|gb|KY425639.1| Zaire ebolavirus isolate IRF0175, partial genome
length: 18880
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1129866655|gb|KY425637.1| Zaire ebolavirus isolate IRF0176, partial genome
length: 18911
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1129866645|gb|KY425636.1| Zaire ebolavirus isolate IRF0190, partial genome
length: 18909
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|1129866607|gb|KY425630.1| Zaire ebolavirus isolate IRF0156, partial genome
length: 18917
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427286|gb|KU321204.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-0776D9 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 8127
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427283|gb|KU321203.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-1305D7 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 8127
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427280|gb|KU321202.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-1302D9 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 8127
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427277|gb|KU321201.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-2807D5 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 16787
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427274|gb|KU321200.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-2571D7 membrane-associated protein VP24 (VP24) and polymerase (L) genes, complete cds
length: 18400
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427271|gb|KU321199.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-2709D5 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 8127
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427268|gb|KU321198.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-2483D5 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 8127
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427265|gb|KU321197.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-2704D5 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 8127
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427262|gb|KU321196.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-1531D9 membrane-associated protein VP24 (VP24) and polymerase (L) genes, partial cds
length: 7699
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427259|gb|KU321195.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-1282D5 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 7933
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427256|gb|KU321194.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-1509D5 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 8127
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427253|gb|KU321193.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-2807D9 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 16060
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427250|gb|KU321192.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-2780D3 membrane-associated protein VP24 (VP24) and polymerase (L) genes, complete cds
length: 15430
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
*****alignment*****
sequence: gi|973427247|gb|KU321191.1| Zaire ebolavirus isolate Ebola virus/H.sapiens-tc/COD/1995/Kikwit-9510621-2711D5 membrane-associated protein VP24 (VP24) gene, partial cds; and polymerase (L) gene, complete cds
length: 8007
e-value: 5.89602e-29
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCC
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
CATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTTTTTAAATATAGTATTGCCfrom Bio import Entrez
Entrez.email = 'bhagirathi.dsh@gmail.com'print(Entrez.read(Entrez.einfo()))DictElement({'DbList': ['pubmed', 'protein', 'nuccore', 'ipg', 'nucleotide', 'nucgss', 'nucest', 'structure', 'sparcle', 'genome', 'annotinfo', 'assembly', 'bioproject', 'biosample', 'blastdbinfo', 'books', 'cdd', 'clinvar', 'clone', 'gap', 'gapplus', 'grasp', 'dbvar', 'gene', 'gds', 'geoprofiles', 'homologene', 'medgen', 'mesh', 'ncbisearch', 'nlmcatalog', 'omim', 'orgtrack', 'pmc', 'popset', 'probe', 'proteinclusters', 'pcassay', 'biosystems', 'pccompound', 'pcsubstance', 'seqannot', 'snp', 'sra', 'taxonomy', 'biocollections', 'unigene', 'gencoll', 'gtr']}, attributes={})einfo_handle = Entrez.einfo()einfo_record = Entrez.read(einfo_handle)print(einfo_record)DictElement({'DbList': ['pubmed', 'protein', 'nuccore', 'ipg', 'nucleotide', 'nucgss', 'nucest', 'structure', 'sparcle', 'genome', 'annotinfo', 'assembly', 'bioproject', 'biosample', 'blastdbinfo', 'books', 'cdd', 'clinvar', 'clone', 'gap', 'gapplus', 'grasp', 'dbvar', 'gene', 'gds', 'geoprofiles', 'homologene', 'medgen', 'mesh', 'ncbisearch', 'nlmcatalog', 'omim', 'orgtrack', 'pmc', 'popset', 'probe', 'proteinclusters', 'pcassay', 'biosystems', 'pccompound', 'pcsubstance', 'seqannot', 'snp', 'sra', 'taxonomy', 'biocollections', 'unigene', 'gencoll', 'gtr']}, attributes={})einfo_record['DbList']['pubmed', 'protein', 'nuccore', 'ipg', 'nucleotide', 'nucgss', 'nucest', 'structure', 'sparcle', 'genome', 'annotinfo', 'assembly', 'bioproject', 'biosample', 'blastdbinfo', 'books', 'cdd', 'clinvar', 'clone', 'gap', 'gapplus', 'grasp', 'dbvar', 'gene', 'gds', 'geoprofiles', 'homologene', 'medgen', 'mesh', 'ncbisearch', 'nlmcatalog', 'omim', 'orgtrack', 'pmc', 'popset', 'probe', 'proteinclusters', 'pcassay', 'biosystems', 'pccompound', 'pcsubstance', 'seqannot', 'snp', 'sra', 'taxonomy', 'biocollections', 'unigene', 'gencoll', 'gtr']efetch_handle = Entrez.efetch(db="nucleotide", id="NM_000744.6", rettype="gb", retmode="text")
print(efetch_handle.read())LOCUS NM_000744 5543 bp mRNA linear PRI 21-OCT-2018
DEFINITION Homo sapiens cholinergic receptor nicotinic alpha 4 subunit
(CHRNA4), transcript variant 1, mRNA.
ACCESSION NM_000744
VERSION NM_000744.6
KEYWORDS RefSeq.
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 5543)
AUTHORS Walsh RM Jr, Roh SH, Gharpure A, Morales-Perez CL, Teng J and Hibbs
RE.
TITLE Structural principles of distinct assemblies of the human
alpha4beta2 nicotinic receptor
JOURNAL Nature 557 (7704), 261-265 (2018)
PUBMED 29720657
REMARK GeneRIF: cryoelectron microscopy and the structural principles of
distinct assemblies of the human alpha4beta2 nicotinic receptor
REFERENCE 2 (bases 1 to 5543)
AUTHORS Jeong JE, Rhee JK, Kim TM, Kwak SM, Bang SH, Cho H, Cheon YH, Min
JA, Yoo GS, Kim K, Choi JS, Choi SW and Kim DJ.
TITLE The association between the nicotinic acetylcholine receptor alpha4
subunit gene (CHRNA4) rs1044396 and Internet gaming disorder in
Korean male adults
JOURNAL PLoS ONE 12 (12), e0188358 (2017)
PUBMED 29240768
REMARK GeneRIF: This study demonstrated that rs1044396 of CHRNA4 was
significantly associated with Internet gaming disorder
Publication Status: Online-Only
REFERENCE 3 (bases 1 to 5543)
AUTHORS Sadaghiani S, Ng B, Altmann A, Poline JB, Banaschewski T, Bokde
ALW, Bromberg U, Buchel C, Burke Quinlan E, Conrod P, Desrivieres
S, Flor H, Frouin V, Garavan H, Gowland P, Gallinat J, Heinz A,
Ittermann B, Martinot JL, Paillere Martinot ML, Lemaitre H, Nees F,
Papadopoulos Orfanos D, Paus T, Poustka L, Millenet S, Frohner JH,
Smolka MN, Walter H, Whelan R, Schumann G, Napolioni V and Greicius
M.
TITLE Overdominant Effect of a CHRNA4 Polymorphism on Cingulo-Opercular
Network Activity and Cognitive Control
JOURNAL J. Neurosci. 37 (40), 9657-9666 (2017)
PUBMED 28877969
REMARK GeneRIF: A polymorphism in CHRNA4 leads to an overdominant effect
at this locus, with higher activity in the cingulo-opercular
network underlying alertness.
REFERENCE 4 (bases 1 to 5543)
AUTHORS Quan J, Ong ML, Bureau JF, Sim LW, Sanmugam S, Abdul Malik AB, Wong
E, Wong J, Chong YS, Saw SM, Kwek K, Qiu A, Holbrook JD and
Rifkin-Graboi A.
CONSRTM GUSTO Study Group
TITLE The influence of CHRNA4, COMT, and maternal sensitivity on
orienting and executive attention in 6-month-old infants
JOURNAL Brain Cogn 116, 17-28 (2017)
PUBMED 28582665
REMARK GeneRIF: Orienting attention predicted by CHRNA4 and maternal
sensitivity interaction in 6-month-old infants.
REFERENCE 5 (bases 1 to 5543)
AUTHORS Eggert M, Aichinger E, Pfaffl MW, Steinlein OK and Pfob M.
TITLE Nicotinic acetylcholine receptor subunits alpha4 and alpha5
associated with smoking behaviour and lung cancer are regulated by
upstream open reading frames
JOURNAL PLoS ONE 8 (7), e66157 (2013)
PUBMED 23843950
REMARK GeneRIF: Nicotinic acetylcholine receptor subunits alpha4 and
alpha5 associated with smoking behavior and lung cancer are
regulated by upstream open reading frames.
Publication Status: Online-Only
REFERENCE 6 (bases 1 to 5543)
AUTHORS Phillips,H.A., Scheffer,I.E., Berkovic,S.F., Hollway,G.E.,
Sutherland,G.R. and Mulley,J.C.
TITLE Localization of a gene for autosomal dominant nocturnal frontal
lobe epilepsy to chromosome 20q 13.2
JOURNAL Nat. Genet. 10 (1), 117-118 (1995)
PUBMED 7647781
REFERENCE 7 (bases 1 to 5543)
AUTHORS Kurahashi,H. and Hirose,S.
TITLE Autosomal Dominant Nocturnal Frontal Lobe Epilepsy
JOURNAL (in) Adam MP, Ardinger HH, Pagon RA, Wallace SE, Bean LJH, Stephens
K and Amemiya A (Eds.);
GENEREVIEWS((R));
(1993)
PUBMED 20301348
REFERENCE 8 (bases 1 to 5543)
AUTHORS Pilz AJ, Willer E, Povey S and Abbott CM.
TITLE The genes coding for phosphoenolpyruvate carboxykinase-1 (PCK1) and
neuronal nicotinic acetylcholine receptor alpha 4 subunit (CHRNA4)
map to human chromosome 20, extending the known region of homology
with mouse chromosome 2
JOURNAL Ann. Hum. Genet. 56 (4), 289-293 (1992)
PUBMED 1492743
REFERENCE 9 (bases 1 to 5543)
AUTHORS Anand R and Lindstrom J.
TITLE Chromosomal localization of seven neuronal nicotinic acetylcholine
receptor subunit genes in humans
JOURNAL Genomics 13 (4), 962-967 (1992)
PUBMED 1505988
REFERENCE 10 (bases 1 to 5543)
AUTHORS McLane KE, Wu XD and Conti-Tronconi BM.
TITLE Identification of a brain acetylcholine receptor alpha subunit able
to bind alpha-bungarotoxin
JOURNAL J. Biol. Chem. 265 (17), 9816-9824 (1990)
PUBMED 2351675
COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
reference sequence was derived from U62433.1, AL121827.34,
L35901.1, BC096291.1, AK296430.1 and AB209359.1.
This sequence is a reference standard in the RefSeqGene project.
On Feb 10, 2012 this sequence version replaced NM_000744.5.
Summary: This gene encodes a nicotinic acetylcholine receptor,
which belongs to a superfamily of ligand-gated ion channels that
play a role in fast signal transmission at synapses. These
pentameric receptors can bind acetylcholine, which causes an
extensive change in conformation that leads to the opening of an
ion-conducting channel across the plasma membrane. This protein is
an integral membrane receptor subunit that can interact with either
nAChR beta-2 or nAChR beta-4 to form a functional receptor.
Mutations in this gene cause nocturnal frontal lobe epilepsy type
1. Polymorphisms in this gene that provide protection against
nicotine addiction have been described. Alternative splicing
results in multiple transcript variants. [provided by RefSeq, Feb
2012].
Transcript Variant: This variant (1) encodes the longer isoform
(1).
Sequence Note: This RefSeq record was created from transcript and
genomic sequence data to make the sequence consistent with the
reference genome assembly. The genomic coordinates used for the
transcript record were based on transcript alignments.
Publication Note: This RefSeq record includes a subset of the
publications that are available for this gene. Please see the Gene
record to access additional publications.
##Evidence-Data-START##
Transcript exon combination :: U62433.1, BC096290.1 [ECO:0000332]
RNAseq introns :: single sample supports all introns
SAMEA1968968, SAMEA2145743
[ECO:0000348]
##Evidence-Data-END##
##RefSeq-Attributes-START##
regulatory uORF :: PMID: 23843950
##RefSeq-Attributes-END##
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-48 U62433.1 1-48
49-53 AL121827.34 130846-130850 c
54-1859 L35901.1 1-1806
1860-2259 BC096291.1 1676-2075
2260-2648 AK296430.1 531-919
2649-2649 AL121827.34 115706-115706 c
2650-4784 AB209359.1 3067-5201
4785-5543 AL121827.34 112812-113570 c
FEATURES Location/Qualifiers
source 1..5543
/organism="Homo sapiens"
/mol_type="mRNA"
/db_xref="taxon:9606"
/chromosome="20"
/map="20q13.33"
gene 1..5543
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/note="cholinergic receptor nicotinic alpha 4 subunit"
/db_xref="GeneID:1137"
/db_xref="HGNC:HGNC:1958"
/db_xref="MIM:118504"
exon 1..307
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/inference="alignment:Splign:2.1.0"
regulatory 151..210
/regulatory_class="other"
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/experiment="DESCRIPTION:regulatory uORF[PMID:23843950]"
/note="regulatory uORF; this uORF is predicted to encode a
19 aa peptide (PMID:23843950)"
misc_feature 208..210
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/note="upstream in-frame stop codon"
CDS 232..2115
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/note="isoform 1 precursor is encoded by transcript
variant 1; cholinergic receptor, nicotinic, alpha
polypeptide 4; neuronal acetylcholine receptor subunit
alpha-4; neuronal nicotinic acetylcholine receptor alpha-4
subunit; cholinergic receptor, nicotinic, alpha 4
(neuronal); cholinergic receptor, nicotinic alpha 4"
/codon_start=1
/product="neuronal acetylcholine receptor subunit alpha-4
isoform 1 precursor"
/protein_id="NP_000735.1"
/db_xref="CCDS:CCDS13517.1"
/db_xref="GeneID:1137"
/db_xref="HGNC:HGNC:1958"
/db_xref="MIM:118504"
/translation="MELGGPGAPRLLPPLLLLLGTGLLRASSHVETRAHAEERLLKKL
FSGYNKWSRPVANISDVVLVRFGLSIAQLIDVDEKNQMMTTNVWVKQEWHDYKLRWDP
ADYENVTSIRIPSELIWRPDIVLYNNADGDFAVTHLTKAHLFHDGRVQWTPPAIYKSS
CSIDVTFFPFDQQNCTMKFGSWTYDKAKIDLVNMHSRVDQLDFWESGEWVIVDAVGTY
NTRKYECCAEIYPDITYAFVIRRLPLFYTINLIIPCLLISCLTVLVFYLPSECGEKIT
LCISVLLSLTVFLLLITEIIPSTSLVIPLIGEYLLFTMIFVTLSIVITVFVLNVHHRS
PRTHTMPTWVRRVFLDIVPRLLLMKRPSVVKDNCRRLIESMHKMASAPRFWPEPEGEP
PATSGTQSLHPPSPSFCVPLDVPAEPGPSCKSPSDQLPPQQPLEAEKASPHPSPGPCR
PPHGTQAPGLAKARSLSVQHMSSPGEAVEGGVRCRSRSIQYCVPRDDAAPEADGQAAG
ALASRNTHSAELPPPDQPSPCKCTCKKEPSSVSPSATVKTRSTKAPPPHLPLSPALTR
AVEGVQYIADHLKAEDTDFSVKEDWKYVAMVIDRIFLWMFIIVCLLGTVGLFLPPWLA
GMI"
sig_peptide 232..315
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/experiment="experimental evidence, no additional details
recorded"
/note="{ECO:0000255}; propagated from UniProtKB/Swiss-Prot
(P43681.2)"
mat_peptide 316..2112
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/product="Neuronal acetylcholine receptor subunit alpha-4"
/experiment="experimental evidence, no additional details
recorded"
/note="propagated from UniProtKB/Swiss-Prot (P43681.2)"
misc_feature 958..1032
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/experiment="experimental evidence, no additional details
recorded"
/note="propagated from UniProtKB/Swiss-Prot (P43681.2);
transmembrane region"
misc_feature 1054..1110
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/experiment="experimental evidence, no additional details
recorded"
/note="propagated from UniProtKB/Swiss-Prot (P43681.2);
transmembrane region"
misc_feature 1156..1221
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/experiment="experimental evidence, no additional details
recorded"
/note="propagated from UniProtKB/Swiss-Prot (P43681.2);
transmembrane region"
misc_feature 1501..1503
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/experiment="experimental evidence, no additional details
recorded"
/note="Phosphoserine. {ECO:0000250|UniProtKB:P09483};
propagated from UniProtKB/Swiss-Prot (P43681.2); other
site"
misc_feature 1843..1845
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/experiment="experimental evidence, no additional details
recorded"
/note="Phosphoserine. {ECO:0000250|UniProtKB:O70174};
propagated from UniProtKB/Swiss-Prot (P43681.2); other
site"
misc_feature 1852..1854
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/experiment="experimental evidence, no additional details
recorded"
/note="Phosphoserine. {ECO:0000250|UniProtKB:O70174};
propagated from UniProtKB/Swiss-Prot (P43681.2); other
site"
misc_feature 2032..2088
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/experiment="experimental evidence, no additional details
recorded"
/note="propagated from UniProtKB/Swiss-Prot (P43681.2);
transmembrane region"
exon 308..459
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/inference="alignment:Splign:2.1.0"
exon 460..504
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/inference="alignment:Splign:2.1.0"
exon 505..614
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/inference="alignment:Splign:2.1.0"
exon 615..1989
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/inference="alignment:Splign:2.1.0"
exon 1990..5543
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/inference="alignment:Splign:2.1.0"
STS 2960..3821
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/standard_name="CHRNA4_1625"
/db_xref="UniSTS:280498"
STS 3362..3517
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/standard_name="RH70691"
/db_xref="UniSTS:91561"
STS 3690..3819
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/standard_name="D20S127E"
/db_xref="UniSTS:77874"
STS 3712..3824
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/standard_name="RH64135"
/db_xref="UniSTS:85131"
STS 4237..4416
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/standard_name="RH75305"
/db_xref="UniSTS:85424"
STS 4579..4703
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/standard_name="RH12050"
/db_xref="UniSTS:90455"
regulatory 4758..4763
/regulatory_class="polyA_signal_sequence"
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
polyA_site 4785
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
STS 5239..5380
/gene="CHRNA4"
/gene_synonym="BFNC; EBN; EBN1; NACHR; NACHRA4; NACRA4"
/standard_name="RH78607"
/db_xref="UniSTS:87070"
ORIGIN
1 tcccagccgg ctgaggcggg cagggccggg cggggccgcg ccacggagcc cacagcccgg
61 cgctccctgc cgcgccgccg ccgcaccgcg ccccacagga gaagacgaac cgggcccggc
121 ggccgaagcg gcccgcgagg cgcgggaggc atgaagttgg gcgcgcacgg gcctcgaagc
181 ggcggggagc cgggagccgc ccgcatctag agcccgcgag gtgcgtgcgc catggagcta
241 gggggccccg gagcgccgcg gctgctgccg ccgctgctgc tgcttctggg gaccggcctc
301 ctgcgcgcca gcagccatgt ggagacccgg gcccacgccg aggagcggct cctgaagaaa
361 ctcttctccg gttacaacaa gtggtcccga cccgtggcca acatctcgga cgtggtcctc
421 gtccgcttcg gcctgtccat cgctcagctc attgacgtgg atgagaagaa ccagatgatg
481 accacgaacg tatgggtgaa gcaggagtgg cacgactaca agctgcgctg ggacccagct
541 gactatgaga atgtcacctc catccgcatc ccctccgagc tcatctggcg gccggacatc
601 gtcctctaca acaatgctga cggggacttc gcggtcaccc acctgaccaa ggcccacctg
661 ttccatgacg ggcgggtgca gtggactccc ccggccattt acaagagctc ctgcagcatc
721 gacgtcacct tcttcccctt cgaccagcag aactgcacca tgaaattcgg ctcctggacc
781 tacgacaagg ccaagatcga cctggtgaac atgcacagcc gcgtggacca gctggacttc
841 tgggagagtg gcgagtgggt catcgtggat gccgtgggca cctacaacac caggaagtac
901 gagtgctgtg ccgagatcta cccggacatc acctatgcct tcgtcatccg gcggctgccg
961 ctcttctaca ccatcaacct catcatcccc tgcctgctca tctcctgcct caccgtgctg
1021 gtcttctacc tgccctccga gtgtggcgag aagatcacgc tgtgcatctc cgtgctgctg
1081 tcgctcaccg tcttcctgct gctcatcacc gagatcatcc cgtccacctc actggtcatc
1141 ccactcatcg gcgagtacct gctgttcacc atgatcttcg tcaccctgtc catcgtcatc
1201 acggtcttcg tgctcaacgt gcaccaccgc tcgccacgca cgcacaccat gcccacctgg
1261 gtacgcaggg tcttcctgga catcgtgcca cgcctgctcc tcatgaagcg gccgtccgtg
1321 gtcaaggaca attgccggcg gctcatcgag tccatgcata agatggccag tgccccgcgc
1381 ttctggcccg agccagaagg ggagccccct gccacgagcg gcacccagag cctgcacccg
1441 ccctcaccgt ccttctgtgt ccccctggat gtgccggctg agcctgggcc ttcctgcaag
1501 tcaccctccg accagctccc tcctcagcag cccctggaag ctgagaaagc cagcccccac
1561 ccctcgcctg gaccctgccg cccgccccac ggcacccagg caccagggct ggccaaagcc
1621 aggtccctca gcgtccagca catgtccagc cctggcgaag cggtggaagg cggcgtccgg
1681 tgccggtctc ggagcatcca gtactgtgtt ccccgagacg atgccgcccc cgaggcagat
1741 ggccaggctg ccggcgccct ggcctctcgc aacacccact cggctgagct cccaccccca
1801 gaccagccct ctccgtgcaa atgcacatgc aagaaggagc cctcttcggt gtccccgagc
1861 gccacggtca agacccgcag caccaaagcg ccgcccccgc acctgcccct gtcgccggcc
1921 ctgacccggg cggtggaggg cgtccagtac attgcagacc acctgaaggc cgaagacaca
1981 gacttctcgg tgaaggagga ctggaagtac gtggccatgg tcatcgaccg catcttcctc
2041 tggatgttca tcatcgtctg cctgctgggg acggtgggcc tcttcctgcc gccctggctg
2101 gctggcatga tctaggaagg gaccgggagc ctgcgtggcc tggggctgcc gtgcacgggg
2161 ccagcatcca tgcggccggc ctggggccgg gctggcttct ccctggactc tgtggggcca
2221 cacgtttgcc aaattttcct tcctgttctg tgtctgctgt aagacggcct tggacgggga
2281 cacggcctct ggggagaccg agtgtggagc tgcttccagt tggactgtgg cctcaggagg
2341 cagtggcttg gagcagaggt gggggtcggc gccttctacc tgcaggactc gggctaagtc
2401 cagttcaaga gtctcctgag ctcccctgca gatggaactc actcctccca gtctctcagc
2461 agatctggtg atggtcccga ccgccccaag gggcccttga agggagttca cgccccttca
2521 gccccaagcg ccccgtcttc tggaggcccg gccgcctctc ccacccaccg tgtcctgcgc
2581 ctgtgtgggc ttcaacttct cccccagggt ccttgagcct ctcgggcccc atgagggtga
2641 gccagcagcg ctccaatctg cttcgctagg agagggtcca ggcagggatt gtgtttggtt
2701 gtgttttggg taagttagtg agaactcaag tcttgtgcct aaggagcctt ggagaacaga
2761 gttttgtgga gctggttccg cgtggggaga atcgggaggc ccacgcggga ccagctctcc
2821 cctgcgcagg ccctccgcgg gggacaggaa cacccagccc cagcgagtct ggagaccagg
2881 actctgcctt ccaggcgtag ggccagggct ctggcaggtg gccagggctc cacgggggcc
2941 tagtggcttc agcccctggg gtacttctgt gttgtgattc cccggagctg ggaaggtccc
3001 gaatggagtc cagacctggg ccctggttcc cccaggaccc tgagggtttc caccttggcg
3061 cgcagcccgg gagatccgcc ctgggctctg ggttcgggaa gaaggacttc ctgctacagt
3121 agctgtgggg agctggtggg ggcatccttg aggacctcca cctgggagat gctgggaccc
3181 tcggggcagg aagtccctga gaagcctcat gggagtcagg gagccctggg gtttccacac
3241 aggcccatgc cctccgtcct ggcagggcag gcagagctca gcacagcctc acccctgcag
3301 gcggtatcca gaggtgaggg aggcctgaaa tgtttccagg catgaccctg gagcccggca
3361 gtgcaccccc taaagatggc gcacccggca gccccccagt gtccccaggg gcacacttcc
3421 ccttgggatg ggcacaggct gccccacccc tccatgattc caagggccca gaggggcggg
3481 gccaggatgg cgtgtcccct gcctgtgagt gacatcggtt caggaggaga cagtcaggaa
3541 gcctcctgct gagtggtcca cattctgctg cccccagacc ccatccagcc aggggtgggg
3601 atggggttgg gctctgcgtc ccactgagtc tcattcctct gtccccgagc cgagctctcc
3661 tgggccaggg tctcgtcagg aggtgcctga gagcagaatg aataattgag gttaggaacc
3721 cggcatgccg agtgccccag aaatgccgct gtgtccccgc gggcagtgac gtgagtgggg
3781 aggagactca ggcccacatt gcccacacct gcctctgaac tgctgctggt cacccccacc
3841 cccgggtgcc tgtgaccggg gtcctgaggc tggggctttt gtgccaggag tgggtgggac
3901 acagagaccc ccgtgccaaa tcctgggcat ccccagcccc ctggcccctc ccacatcccc
3961 cgtgtattca ggaccccatc tgctgagctc tgacctgccc ccgctctgcc atcagcccct
4021 gctgctcctc ggccagagct cccaggacgc agggagaccc tgggagagtg aggtcatccc
4081 ggggccatgg aagctggcag gagacactgg tctcagagga gggatagaga cgcagatttc
4141 agatgtaaga agcccgatcc acattgcata agtggaccca gctgccagat gtgtgggcag
4201 ctgcagggag tggcccgggg tgctgggccc agctgtggtt gttcttttct gggtcaggag
4261 tgactgcgga gtggctggga cgctcctgcc gggggaccct cctgccgggg gtggccgctt
4321 gcctggggga agaccccttt ccctttcttt ttttttttga ggctcaaaaa aaaaatccaa
4381 ataaagcacc atattcccac cacgccaaat taaccttgac aacaatgttg gcgtatttgc
4441 gtccagtgct gtttttatta attaaggtaa aatttacata tggtgagatg catgctcttc
4501 agtggagacc cagcccctag aaggtccctc cagcccttcc tgtcggcgtc cctccccatc
4561 tgtggctctg acttaagcac cgtggattga cctctccggc tcacgacctt cgaggagtca
4621 gaatcctgca gttggagcct ttgatgtctg gcttcttcat cctatgactt agagcttcat
4681 ccgtgctgtt gtgtgtgtcc gtagctcctt gctgtctgtt ccttcgtttt taattgtgag
4741 cagtgttctt ctgtctgaat aaactaagac gcagtttgtc catcacctgt tagtggactt
4801 tgcttgcagc tgtcggtgat taggaatgga ggtgccggtg tgtgcatggc actctatccg
4861 ttatgcatgt ttattttctg catctgttaa tgttttaaca tctttcagac ccaggactgc
4921 tcctcctagg gccagttagt tcccgggggt ggacagcttg cctagaaccc accttgccag
4981 ggctgtgacc cccgaccccc tatcaaagtc tcacactaag ccaacgtttc cccgccctgt
5041 gccaggcacc aggcagcggg agacactgct gcagctcgaa gcctgccggg gcgccggccc
5101 ctctgcggct gcttgcgcca tcctgccccc tccttcccag gggaggcccc agtgaaggcc
5161 ctggccaggg cttcccagcc ccttctgcct ccggaccggc ctgggtgctt cccgtgtggc
5221 ccggcctggg gcgacgtggc cctcctctca ggaagcgtgg taatctctca atggctggcc
5281 tccggagttg tcactcaggc tcccttgtaa gttaaggccg ggcccaggac actctagggc
5341 acgcagctgc tgtgggactg ctgggttagg tgtcccctgg agcagaggcg gcttcggatt
5401 tctaaagtgg ctgagtcctt tcaccttgca ccagaaatgc tggatcaggc gcagcacaca
5461 cagcacctgg ggatgcaagc ccggccagcc ccatggacca agccccgccg accgtgtggc
5521 ccgccgagcc caggtgcggc cgc
//fasta_handle = Entrez.efetch(db="nucleotide", id="NM_000744.6", rettype="fasta", retmode="text")
print(fasta_handle.read())>NM_000744.6 Homo sapiens cholinergic receptor nicotinic alpha 4 subunit (CHRNA4), transcript variant 1, mRNA
TCCCAGCCGGCTGAGGCGGGCAGGGCCGGGCGGGGCCGCGCCACGGAGCCCACAGCCCGGCGCTCCCTGC
CGCGCCGCCGCCGCACCGCGCCCCACAGGAGAAGACGAACCGGGCCCGGCGGCCGAAGCGGCCCGCGAGG
CGCGGGAGGCATGAAGTTGGGCGCGCACGGGCCTCGAAGCGGCGGGGAGCCGGGAGCCGCCCGCATCTAG
AGCCCGCGAGGTGCGTGCGCCATGGAGCTAGGGGGCCCCGGAGCGCCGCGGCTGCTGCCGCCGCTGCTGC
TGCTTCTGGGGACCGGCCTCCTGCGCGCCAGCAGCCATGTGGAGACCCGGGCCCACGCCGAGGAGCGGCT
CCTGAAGAAACTCTTCTCCGGTTACAACAAGTGGTCCCGACCCGTGGCCAACATCTCGGACGTGGTCCTC
GTCCGCTTCGGCCTGTCCATCGCTCAGCTCATTGACGTGGATGAGAAGAACCAGATGATGACCACGAACG
TATGGGTGAAGCAGGAGTGGCACGACTACAAGCTGCGCTGGGACCCAGCTGACTATGAGAATGTCACCTC
CATCCGCATCCCCTCCGAGCTCATCTGGCGGCCGGACATCGTCCTCTACAACAATGCTGACGGGGACTTC
GCGGTCACCCACCTGACCAAGGCCCACCTGTTCCATGACGGGCGGGTGCAGTGGACTCCCCCGGCCATTT
ACAAGAGCTCCTGCAGCATCGACGTCACCTTCTTCCCCTTCGACCAGCAGAACTGCACCATGAAATTCGG
CTCCTGGACCTACGACAAGGCCAAGATCGACCTGGTGAACATGCACAGCCGCGTGGACCAGCTGGACTTC
TGGGAGAGTGGCGAGTGGGTCATCGTGGATGCCGTGGGCACCTACAACACCAGGAAGTACGAGTGCTGTG
CCGAGATCTACCCGGACATCACCTATGCCTTCGTCATCCGGCGGCTGCCGCTCTTCTACACCATCAACCT
CATCATCCCCTGCCTGCTCATCTCCTGCCTCACCGTGCTGGTCTTCTACCTGCCCTCCGAGTGTGGCGAG
AAGATCACGCTGTGCATCTCCGTGCTGCTGTCGCTCACCGTCTTCCTGCTGCTCATCACCGAGATCATCC
CGTCCACCTCACTGGTCATCCCACTCATCGGCGAGTACCTGCTGTTCACCATGATCTTCGTCACCCTGTC
CATCGTCATCACGGTCTTCGTGCTCAACGTGCACCACCGCTCGCCACGCACGCACACCATGCCCACCTGG
GTACGCAGGGTCTTCCTGGACATCGTGCCACGCCTGCTCCTCATGAAGCGGCCGTCCGTGGTCAAGGACA
ATTGCCGGCGGCTCATCGAGTCCATGCATAAGATGGCCAGTGCCCCGCGCTTCTGGCCCGAGCCAGAAGG
GGAGCCCCCTGCCACGAGCGGCACCCAGAGCCTGCACCCGCCCTCACCGTCCTTCTGTGTCCCCCTGGAT
GTGCCGGCTGAGCCTGGGCCTTCCTGCAAGTCACCCTCCGACCAGCTCCCTCCTCAGCAGCCCCTGGAAG
CTGAGAAAGCCAGCCCCCACCCCTCGCCTGGACCCTGCCGCCCGCCCCACGGCACCCAGGCACCAGGGCT
GGCCAAAGCCAGGTCCCTCAGCGTCCAGCACATGTCCAGCCCTGGCGAAGCGGTGGAAGGCGGCGTCCGG
TGCCGGTCTCGGAGCATCCAGTACTGTGTTCCCCGAGACGATGCCGCCCCCGAGGCAGATGGCCAGGCTG
CCGGCGCCCTGGCCTCTCGCAACACCCACTCGGCTGAGCTCCCACCCCCAGACCAGCCCTCTCCGTGCAA
ATGCACATGCAAGAAGGAGCCCTCTTCGGTGTCCCCGAGCGCCACGGTCAAGACCCGCAGCACCAAAGCG
CCGCCCCCGCACCTGCCCCTGTCGCCGGCCCTGACCCGGGCGGTGGAGGGCGTCCAGTACATTGCAGACC
ACCTGAAGGCCGAAGACACAGACTTCTCGGTGAAGGAGGACTGGAAGTACGTGGCCATGGTCATCGACCG
CATCTTCCTCTGGATGTTCATCATCGTCTGCCTGCTGGGGACGGTGGGCCTCTTCCTGCCGCCCTGGCTG
GCTGGCATGATCTAGGAAGGGACCGGGAGCCTGCGTGGCCTGGGGCTGCCGTGCACGGGGCCAGCATCCA
TGCGGCCGGCCTGGGGCCGGGCTGGCTTCTCCCTGGACTCTGTGGGGCCACACGTTTGCCAAATTTTCCT
TCCTGTTCTGTGTCTGCTGTAAGACGGCCTTGGACGGGGACACGGCCTCTGGGGAGACCGAGTGTGGAGC
TGCTTCCAGTTGGACTGTGGCCTCAGGAGGCAGTGGCTTGGAGCAGAGGTGGGGGTCGGCGCCTTCTACC
TGCAGGACTCGGGCTAAGTCCAGTTCAAGAGTCTCCTGAGCTCCCCTGCAGATGGAACTCACTCCTCCCA
GTCTCTCAGCAGATCTGGTGATGGTCCCGACCGCCCCAAGGGGCCCTTGAAGGGAGTTCACGCCCCTTCA
GCCCCAAGCGCCCCGTCTTCTGGAGGCCCGGCCGCCTCTCCCACCCACCGTGTCCTGCGCCTGTGTGGGC
TTCAACTTCTCCCCCAGGGTCCTTGAGCCTCTCGGGCCCCATGAGGGTGAGCCAGCAGCGCTCCAATCTG
CTTCGCTAGGAGAGGGTCCAGGCAGGGATTGTGTTTGGTTGTGTTTTGGGTAAGTTAGTGAGAACTCAAG
TCTTGTGCCTAAGGAGCCTTGGAGAACAGAGTTTTGTGGAGCTGGTTCCGCGTGGGGAGAATCGGGAGGC
CCACGCGGGACCAGCTCTCCCCTGCGCAGGCCCTCCGCGGGGGACAGGAACACCCAGCCCCAGCGAGTCT
GGAGACCAGGACTCTGCCTTCCAGGCGTAGGGCCAGGGCTCTGGCAGGTGGCCAGGGCTCCACGGGGGCC
TAGTGGCTTCAGCCCCTGGGGTACTTCTGTGTTGTGATTCCCCGGAGCTGGGAAGGTCCCGAATGGAGTC
CAGACCTGGGCCCTGGTTCCCCCAGGACCCTGAGGGTTTCCACCTTGGCGCGCAGCCCGGGAGATCCGCC
CTGGGCTCTGGGTTCGGGAAGAAGGACTTCCTGCTACAGTAGCTGTGGGGAGCTGGTGGGGGCATCCTTG
AGGACCTCCACCTGGGAGATGCTGGGACCCTCGGGGCAGGAAGTCCCTGAGAAGCCTCATGGGAGTCAGG
GAGCCCTGGGGTTTCCACACAGGCCCATGCCCTCCGTCCTGGCAGGGCAGGCAGAGCTCAGCACAGCCTC
ACCCCTGCAGGCGGTATCCAGAGGTGAGGGAGGCCTGAAATGTTTCCAGGCATGACCCTGGAGCCCGGCA
GTGCACCCCCTAAAGATGGCGCACCCGGCAGCCCCCCAGTGTCCCCAGGGGCACACTTCCCCTTGGGATG
GGCACAGGCTGCCCCACCCCTCCATGATTCCAAGGGCCCAGAGGGGCGGGGCCAGGATGGCGTGTCCCCT
GCCTGTGAGTGACATCGGTTCAGGAGGAGACAGTCAGGAAGCCTCCTGCTGAGTGGTCCACATTCTGCTG
CCCCCAGACCCCATCCAGCCAGGGGTGGGGATGGGGTTGGGCTCTGCGTCCCACTGAGTCTCATTCCTCT
GTCCCCGAGCCGAGCTCTCCTGGGCCAGGGTCTCGTCAGGAGGTGCCTGAGAGCAGAATGAATAATTGAG
GTTAGGAACCCGGCATGCCGAGTGCCCCAGAAATGCCGCTGTGTCCCCGCGGGCAGTGACGTGAGTGGGG
AGGAGACTCAGGCCCACATTGCCCACACCTGCCTCTGAACTGCTGCTGGTCACCCCCACCCCCGGGTGCC
TGTGACCGGGGTCCTGAGGCTGGGGCTTTTGTGCCAGGAGTGGGTGGGACACAGAGACCCCCGTGCCAAA
TCCTGGGCATCCCCAGCCCCCTGGCCCCTCCCACATCCCCCGTGTATTCAGGACCCCATCTGCTGAGCTC
TGACCTGCCCCCGCTCTGCCATCAGCCCCTGCTGCTCCTCGGCCAGAGCTCCCAGGACGCAGGGAGACCC
TGGGAGAGTGAGGTCATCCCGGGGCCATGGAAGCTGGCAGGAGACACTGGTCTCAGAGGAGGGATAGAGA
CGCAGATTTCAGATGTAAGAAGCCCGATCCACATTGCATAAGTGGACCCAGCTGCCAGATGTGTGGGCAG
CTGCAGGGAGTGGCCCGGGGTGCTGGGCCCAGCTGTGGTTGTTCTTTTCTGGGTCAGGAGTGACTGCGGA
GTGGCTGGGACGCTCCTGCCGGGGGACCCTCCTGCCGGGGGTGGCCGCTTGCCTGGGGGAAGACCCCTTT
CCCTTTCTTTTTTTTTTTGAGGCTCAAAAAAAAAATCCAAATAAAGCACCATATTCCCACCACGCCAAAT
TAACCTTGACAACAATGTTGGCGTATTTGCGTCCAGTGCTGTTTTTATTAATTAAGGTAAAATTTACATA
TGGTGAGATGCATGCTCTTCAGTGGAGACCCAGCCCCTAGAAGGTCCCTCCAGCCCTTCCTGTCGGCGTC
CCTCCCCATCTGTGGCTCTGACTTAAGCACCGTGGATTGACCTCTCCGGCTCACGACCTTCGAGGAGTCA
GAATCCTGCAGTTGGAGCCTTTGATGTCTGGCTTCTTCATCCTATGACTTAGAGCTTCATCCGTGCTGTT
GTGTGTGTCCGTAGCTCCTTGCTGTCTGTTCCTTCGTTTTTAATTGTGAGCAGTGTTCTTCTGTCTGAAT
AAACTAAGACGCAGTTTGTCCATCACCTGTTAGTGGACTTTGCTTGCAGCTGTCGGTGATTAGGAATGGA
GGTGCCGGTGTGTGCATGGCACTCTATCCGTTATGCATGTTTATTTTCTGCATCTGTTAATGTTTTAACA
TCTTTCAGACCCAGGACTGCTCCTCCTAGGGCCAGTTAGTTCCCGGGGGTGGACAGCTTGCCTAGAACCC
ACCTTGCCAGGGCTGTGACCCCCGACCCCCTATCAAAGTCTCACACTAAGCCAACGTTTCCCCGCCCTGT
GCCAGGCACCAGGCAGCGGGAGACACTGCTGCAGCTCGAAGCCTGCCGGGGCGCCGGCCCCTCTGCGGCT
GCTTGCGCCATCCTGCCCCCTCCTTCCCAGGGGAGGCCCCAGTGAAGGCCCTGGCCAGGGCTTCCCAGCC
CCTTCTGCCTCCGGACCGGCCTGGGTGCTTCCCGTGTGGCCCGGCCTGGGGCGACGTGGCCCTCCTCTCA
GGAAGCGTGGTAATCTCTCAATGGCTGGCCTCCGGAGTTGTCACTCAGGCTCCCTTGTAAGTTAAGGCCG
GGCCCAGGACACTCTAGGGCACGCAGCTGCTGTGGGACTGCTGGGTTAGGTGTCCCCTGGAGCAGAGGCG
GCTTCGGATTTCTAAAGTGGCTGAGTCCTTTCACCTTGCACCAGAAATGCTGGATCAGGCGCAGCACACA
CAGCACCTGGGGATGCAAGCCCGGCCAGCCCCATGGACCAAGCCCCGCCGACCGTGTGGCCCGCCGAGCC
CAGGTGCGGCCGChschrna4_handle = Entrez.esearch(db="nucleotide", term="Homo sapiens[Orgn] AND CHRNA4[Gene]", idtype="acc")
hschrna4_record = Entrez.read(hschrna4_handle)
hschrna4_record["Count"]'43'hschrna4_record["IdList"]['NR_046317.1', 'NM_001256573.1', 'NM_000744.6', 'NG_011931.1', 'XM_024451822.1', 'XM_017027625.2', 'XM_011528524.1', 'NC_000020.11', 'AY878244.1', 'AY878243.1', 'AY816234.1', 'KR711794.1', 'KR711793.1', 'KR711792.1', 'KR711791.1', 'CM000271.1', 'CH471077.2', 'BC096293.3', 'BC096290.1', 'BC096292.1']# nicotinic search
handle = Entrez.esearch(db="nucleotide", term="nicotinic", retmax=50, type="acc")
record = Entrez.read(handle)
handle.close
print(record.keys())dict_keys(['IdList', 'TranslationSet', 'RetMax', 'RetStart', 'QueryTranslation', 'TranslationStack', 'Count'])print(record['IdList'])['1523147790', '1523145344', '1523142829', '1523133633', '1523131203', '1523116150', '1523113138', '1523112708', '1523103732', '1523092346', '1523091109', '1523080985', '1523080122', '1523069848', '1523063454', '1523057334', '1523053879', '1523051942', '1523044822', '1523024007', '1523023669', '1523018785', '1523017557', '1523016273', '1523004522', '1522997402', '1522993495', '1522982347', '1522981058', '1522971555', '1522966821', '1522962555', '1522949757', '1522944298', '1522933472', '1522931349', '1522918912', '1522872626', '1522872346', '1522866699', '1522859975', '1522856484', '1522851794', '1522850987', '1522839685', '1522832792', '1522832095', '1522824605', '1522820868', '1522809651']#Texas AND hydra vulgaris search
handle = Entrez.esearch(db="nuccore", term="Texas AND hydra vulgaris")
record = Entrez.read(handle)
gi_list = record["IdList"]
print(gi_list)['1215461482', '83595176', '83595170', '83595168', '83595164', '83595162', '83595158', '83595156', '83595154', '83595152', '830260241', '830260300', '830260278', '830260045', '401709912', '380765232', '83595174', '83595172', '83595166', '83595134']from Bio import Entrez
handle = Entrez.egquery(term="Ronald Lukas")
record = Entrez.read(handle)
for row in record["eGQueryResult"]:
print(row["DbName"], row["Count"])pubmed 91
pmc 53
mesh 0
books 0
pubmedhealth 2
omim 0
ncbisearch 5
nuccore 5
nucgss 458024
nucest 64594
protein 5
genome 0
structure 0
taxonomy 0
snp 0
dbvar 5
gene 1
sra 0
biosystems 4
unigene 0
cdd 0
clone 0
popset 0
geoprofiles 0
gds 0
homologene 0
pccompound 0
pcsubstance 0
pcassay 1
nlmcatalog 1
probe 0
gap 25438
proteinclusters 0
bioproject 0
biosample 0
biocollections 0import os
import Bio
from Bio import SeqIO
from Bio import Entrez
filename = "NM_000744.6.gbk"
if not os.path.isfile(filename):
# Downloading...
net_handle = Entrez.efetch(db="nucleotide", id="NM_000744.6", rettype="fasta", retmode="text")
out_handle = open(filename, "w")
out_handle.write(net_handle.read())
out_handle.close()
net_handle.close()
print("Saved")
print("Parsing...")
record = SeqIO.read(filename, "genbank")
print(record)Parsing...
ID: NM_000744.6
Name: NM_000744
Description: Homo sapiens cholinergic receptor nicotinic alpha 4 subunit (CHRNA4), transcript variant 1, mRNA
Number of features: 29
/taxonomy=['Eukaryota', 'Metazoa', 'Chordata', 'Craniata', 'Vertebrata', 'Euteleostomi', 'Mammalia', 'Eutheria', 'Euarchontoglires', 'Primates', 'Haplorrhini', 'Catarrhini', 'Hominidae', 'Homo']
/data_file_division=PRI
/keywords=['RefSeq']
/structured_comment=OrderedDict([('Evidence-Data', OrderedDict([('Transcript exon combination', 'U62433.1, BC096290.1 [ECO:0000332]'), ('RNAseq introns', 'single sample supports all introns')])), ('RefSeq-Attributes', OrderedDict([('regulatory uORF', 'PMID: 23843950')]))])
/references=[Reference(title='Structural principles of distinct assemblies of the human alpha4beta2 nicotinic receptor', ...), Reference(title='The association between the nicotinic acetylcholine receptor alpha4 subunit gene (CHRNA4) rs1044396 and Internet gaming disorder in Korean male adults', ...), Reference(title='Overdominant Effect of a CHRNA4 Polymorphism on Cingulo-Opercular Network Activity and Cognitive Control', ...), Reference(title='The influence of CHRNA4, COMT, and maternal sensitivity on orienting and executive attention in 6-month-old infants', ...), Reference(title='Nicotinic acetylcholine receptor subunits alpha4 and alpha5 associated with smoking behaviour and lung cancer are regulated by upstream open reading frames', ...), Reference(title='Localization of a gene for autosomal dominant nocturnal frontal lobe epilepsy to chromosome 20q 13.2', ...), Reference(title='Autosomal Dominant Nocturnal Frontal Lobe Epilepsy', ...), Reference(title='The genes coding for phosphoenolpyruvate carboxykinase-1 (PCK1) and neuronal nicotinic acetylcholine receptor alpha 4 subunit (CHRNA4) map to human chromosome 20, extending the known region of homology with mouse chromosome 2', ...), Reference(title='Chromosomal localization of seven neuronal nicotinic acetylcholine receptor subunit genes in humans', ...), Reference(title='Identification of a brain acetylcholine receptor alpha subunit able to bind alpha-bungarotoxin', ...)]
/sequence_version=6
/comment=REVIEWED REFSEQ: This record has been curated by NCBI staff. The
reference sequence was derived from U62433.1, AL121827.34,
L35901.1, BC096291.1, AK296430.1 and AB209359.1.
This sequence is a reference standard in the RefSeqGene project.
On Feb 10, 2012 this sequence version replaced NM_000744.5.
Summary: This gene encodes a nicotinic acetylcholine receptor,
which belongs to a superfamily of ligand-gated ion channels that
play a role in fast signal transmission at synapses. These
pentameric receptors can bind acetylcholine, which causes an
extensive change in conformation that leads to the opening of an
ion-conducting channel across the plasma membrane. This protein is
an integral membrane receptor subunit that can interact with either
nAChR beta-2 or nAChR beta-4 to form a functional receptor.
Mutations in this gene cause nocturnal frontal lobe epilepsy type
1. Polymorphisms in this gene that provide protection against
nicotine addiction have been described. Alternative splicing
results in multiple transcript variants. [provided by RefSeq, Feb
2012].
Transcript Variant: This variant (1) encodes the longer isoform
(1).
Sequence Note: This RefSeq record was created from transcript and
genomic sequence data to make the sequence consistent with the
reference genome assembly. The genomic coordinates used for the
transcript record were based on transcript alignments.
Publication Note: This RefSeq record includes a subset of the
publications that are available for this gene. Please see the Gene
record to access additional publications.
SAMEA1968968, SAMEA2145743
[ECO:0000348]
/source=Homo sapiens (human)
/organism=Homo sapiens
/topology=linear
/accessions=['NM_000744']
/molecule_type=mRNA
/date=21-OCT-2018
Seq('TCCCAGCCGGCTGAGGCGGGCAGGGCCGGGCGGGGCCGCGCCACGGAGCCCACA...CGC', IUPACAmbiguousDNA())hv_fasta = open('hv_nt_seq.fasta')
hv_fasta.read()'>DQ286061.1 Hydra vulgaris mitochondrial succinate dehydrogenase flavoprotein subunit mRNA, partial cds; nuclear gene for mitochondrial product\nTGTTGTGCTGTTGCTGATCGAACTGGTCATTCACTACTTCATACTCTTTATGGACAGTCATTGCGATACG\nATTGTAACTACTTTATAGAATACTTTGCATTGGATTTGTTGATGGATAAAGGAAAATGTGTTGGGATAAT\nTGCATTAAATCTTGAAGATGGATCTTTGCATAGGATTAAAGCAAAAAATACCGTCCTTGCAACCGGTGGT\nTCTGGAAGAACGTATTTCTCATGTACTTCAGCCCATACATGCACAGGAGATGGCACTGCTATGGTTACAA\nGAGCTGGTCTTGCAAATGAAGATTTAGAGTTCATTCAGTTTCATCCTACTGGTATTTATGGAGCTGGTTG\nTCTCATCACAGAAGGTTGTAGAGGAGAAGGAGGCTACTTGATTAATAGCGAGGGTGAACGCTTTATGGAA\nAGATATGCTCCTACTGCAAAGGATCTTGCCTCAAGAGATGTTGTTTCTCGATCGATGACAATTGAGATGA\nGAGAAGGGCGTGGATGTGGACCTGAAAAAGATCATGTATATTTACAATTGTCTCATCTTCCCCAAGAGAT\nACTTAAATCTCGTCTTCCTGGAATTTCTGAGACAGCCATGATATTTGCTGGTGTTGATGTAACTCGTGAT\nCCTATACCTGTTCTTCCAACTTGCCATTACAATATGGGTGGAATACCAACCAACTTTAACGGACAGGTAA\nTACAACATCATAATGGTAAAGATGTTATTGTGGAAGGTTTGTATGCTGCAGGTGAAGCTGCTTGTGCTTC\nAGTTCATGGTGCTAACCGTCTGGGAGCTAATTCTTTGCTCGATTTAGTCATATTTGGTCGTGCTTGTGCC\nTTAGATATTGCTGCCAAAAATAAGCCTGGAGACAGCATTCCTGATTTACCCAGTGATATTGGTGAAGTAT\nCTGTGGCCAATCTTGATAAGGTTCGGTTTGCCAATGGACACACACCAACTGCAAATTTGAGATTAAAGAT\nGCAAAAGATTATGCAAGGACATGCAGCTGTATTCAGGACTGGTGCTGTCTTGGCAGAAGGAGTGTCAAAG\nATTTATCAGGCTTATGATGAGTTGAAGGATCTTAAGCTTTATGACCGTGGTATGATATTGAATACAGATC\nTTGTTGAAGCTCTGGAACTTCAAAATTTAATGTTAAACTCCTGTCTAGCAATGGTGTCTGCAGAAGCCAG\nAAAAGAAAGTCGTGGTGCGCTT\n\n>DQ286057.1 Hydra vulgaris myosin heavy chain mRNA, partial cds\nTGACAACTTTCTGCTGTTGGGCGCCGGAAAGGTAGTGCTTTTCAAACTGTATCATTTCGTCACAAGGAAC\nAACTAAAAAATTTGCTTACTACTCTTGGAATGACTAGTCCTCATTTCGTAAGATGTATCATTCCTAATGA\nAAAGAAGGAACCAGGAGTTGTTGAGGGCCAACTTGTTCTTCATCAGTTGAGGTGTAATGGTGTCTTGGAA\nGGTATTCGCATATGTAGAAAAGGTTTTCCATCCAGAATGAATTTTCAAGATTTTAAGTTAAGGTACCAAA\nTACTAGCATCTAATGCGATCCCACCTGGTTTTATTGATGGCAAAGTAGCAGCTGAAAAATTAATTGAGGC\nACTTCAACTAGATCAAAGTGAATACAGAGTAGGAAAGACAAAAATATTCTTTAGAGCTGGTATTGTGGGA\nGAGTTAGAAGAAATGCGCGATGAGCGATTATCTAAAATTATTTCACAGTTCCAAGCATACTGTAAGGGCA\nGTATTATGCGCAGTGAATATAAAAAGATGGTGGCACAGCGTATTGGTCTAGCTGTTATTCAAAGAAATGT\nCAGAAAGTATTTATTCTTGCGCCATTGGTCTTGGTGGAAGTTGTACACTAAGGTTCAACCTTTATTGAGT\nGTTGCACGAGCAGAGGATGAAATGAGAGCAAAAGAAGAAGAGTTAGAAGCTGCTAAAGAACAATTAAAAA\nAAGATGCAGAAGCTAAGAAAAAAATGGAAGAAGAACTGACTGAGGCTATGGCTCAAAAAGAAAAACTTTA\nTGCAAGTTTACAAGCTGAGACTGACAGATTAATTACAATTGAAGACAAGCTTCTCAATCTGCAAACAGTT\nAAGGATAAACTTGAAAGTAGTCTAAATGAAGCATTAGAAAAGCTGGATGGAGAAGAACATAGTGTTTTAG\nTTCTTGAAGAAAAGATTCAAGAAGCAGAAGAAAAAATTGACGAACTTACTGAAAAGACTGAGGAACTCCA\nATCAAACATTAGTCGACTTGAAACTGAAAAACAAAATCGTGATAAACAAATTGATACCTTGAATGAAGAT\nATTCGCAAGCAAGATGAAACTATCTCTAAAATGAATGCAGAAAAGAAGCATGTAGATGAGGAGTTGAAAG\nATCGCACTGAACAACTACAGGCTGCTGAGGATAAATGCAACAACCTCAATAAAACAAAGAATAAATTAGA\nATCTTCTATTAGAGAGATTGAACAAGATTTAAAGAAAGAAAAAGACAGTAAAATGAAGTTAGAAAAAGAA\nAAAAAGAAAGTTGAGTCAGATCTTAAAGACAATCGAGATAAACTTTCAGAAACAGAAACTCGTCTAAAAG\nAAACTCAGGATCTTGTAACTAAACGAGAAAAGTCAATATCCGATTTAGAAAATGCAAAAGAAGGTCTTGA\nATCACAGATTAGTCAACTCCAAAGAAAAATACAAGAACTTCTTGCTAAAATTGAAGAATTAGAAGAAGAG\nCTTGAAAACGAAAGAAAGTTGAGGCAGAAATCAGAGCTACAAAGAAAAGAGTTAGAGTCAAGAATTGAGG\nAATTGCAAGACCAACTTGAAACAGCAGGCGGTGCTACATCAGCTCAAGTTGAAGTTGGTAAAAAACGTGA\nAGCTGAATGTAATCGCCTTAGAAAAGAGATTGAAGCCCTTAACATAGCAAATGATGCTGCCATCTCAGCT\nATTAAAGCAAAAACAAATGCTACAATAGCAGAAATTCAAGAGGAAAATGAAGCAATGAAAAAAGCAAAAG\nCAAAACTTGAGAAAGAAAAAAGTGCACTTAATAATGAATTAAATGAAACTAAAAACTCGCTTGATCAAAT\nTAAGAAGCAAAAAACTAATAGTGACAAGAACTCCCGTATGCTTGAAGAACAAATCAATGAACTAAACAGC\nAAGTTGGCTCAAGTTGATGAATTACATTCTCAAAGTGAGTCAAAGAATTCTAAAGTTAACAGTGAGTTGT\nTGGCTCTTAACAGTCAATTGAGCGAATCAGAACATAATTTGGGAATAGCTACTAAAAATATAAAAACTTT\nAGAAAGTCAACTTGCAGAAAGTAAAAATTTTAATGAAGCTGAATCAAAGGCTAAACTTGAGAATTACAAC\nAGCTCGAATGCTTTT\n\n>DQ286058.1 Hydra vulgaris chitinase mRNA, partial cds\nATTGGTCGTTATTGCGGTCAAGGACGTTACCCATTAATGTCTTCAGTGGGTAAACTTCTTGGTGGATACG\nTTCCTCCCGTTGAGCCTACGTTCTCCCCAACCACAAAAGGACCATCAACGCCTAGCAAAAGTAGTACTGC\nCACTGATCGTCCTGCAACAAACCCCCCAACTGGAGCATGTAAGGCAATCGATGCAAGAGTAAAAGATCAA\nTGGTGTAATGATAACTGTCCCAAAGGATATTGCCCTACTGAGTTTTGTAAATGTTAAATAAATAAAAAAA\nGTGTTAACTTATTGCTCTTAAAAAAAAAAAAAAAAAAA\n\n>DQ286055.1 Hydra vulgaris putative solute carrier family 30 mRNA, partial cds\nGAAGTTTAGAATTCTTCCAGACTACTTATTAACAGATTATACTGACAGTAGATGAAAGAAGTTAGTCGGT\nTTACAAATAGTCAAGGAATTAAGATGAAATGTAAGTTTGGCCGAAATGCTACCTTTATTTTAATGTTGGT\nATAACAATGTCATTTTTTATTGTGGAGCTTGTTGTTGGTTATATGACTAAATCAATGGCATTGGTTGCTG\nACTCCTTTCAGATGTTATCGGATACAGTCTCTATTATTGTTGGCTTTGTTGCTTTTCACTGTTCGAAGCG\nTAGTGAAACCTCCAGCCGATTTACATATGGCTGGGTTCGTGCTGAAATACTTGGAGCTTTAGTTAATTCA\nGTATTTCTTGCTGCTCTTTGTTTTACAATTCTCATAGAATCATTTAAGCGGTCTGCTATTCCAGAAAGAG\nTTGAAAATCCTAAACTTGTTCTTATAGTCGGAGCAGTTGGTTTGCTTGTTAATATAATTGGGTTGTTTCT\nTTTTAATCACCACAGTAATGGCCATTCAAATAATAGTGAATCTGTTGAAAAAGGACATAATAATGAAGTT\nGTAGACAATATTGTTGCTGAATTCCCATTAGTTGATAGTAGTGAAGTGGTTATTTATGATAGTGATAAAA\nGCAATTCCCAAGTACCTCAAGTTGTAAGTAATAATGAGAATAGTAAAAAAAAATTAGGAGCATCTCGTCT\nAAATATTCGTGGAGTTTATTTGAATATTCTTGGAGATGCTTTAGGGTCAG\n\n>DQ286054.1 Hydra vulgaris putative solute carrier family 39 member 1 mRNA, partial cds\nTTCTTCAATATTTTAATCAACACAGAAAAAAAATATTTTGACTGTAAAAAAGAAGAATCCTTTTTTAGCT\nATGGGTTTTTATGAATTACCAGAATGGTCAGTTAAACTAATTATAATTATTATTTTATTTTTATTGGGCA\nTGATATTTGGTGTTGTACCATTAAATCTTTCACGAAGCTCCTCATTTGAAGGAAGAGTTTCTCCTACTCG\nCAATCTGCTTATTAGTTTGTCAAATTGCTTTGCTGGAGGGGTGTTTTTTAGCACTGTTATTCTTGATTTA\nTTTCCATTGGTAAAGTTAACAGTAAATAATGCACTAATATCTGTTTATATTGATACTGATTTTCCGCTAG\nGGGATTTTATTATTGGTATTGGATTTATCTTTATGTTAATTTTAGAGCATATAGTTCATTCTTGTTGCCA\nTCCTAATCAGTTATCTTATGAAGCTCCTAAAAATGTTAATAGTAACCAGGATGAATTATCATGTAATGAA\nAATAATCATCTTTTATCTCATGACAACAACTTTGATGTAGTTACTGATATTGAGATAAACACTTCAGAAA\nGACAGCTGCAACAA\n\n>DQ286051.1 Hydra vulgaris ribosomal protein S19 mRNA, partial cds\nCAGCTTTAATGGCCCTCAAGAATTTGTAAAAGCTTTTGCTGGACACCTAAAAAAAGGTAATAAATTTAAA\nGTGCCAGAATTTGTTGAGATAGTAAAAACTTCGAAAGCTTGTGAACTTGGACCTTCTGATCCTGATTGGT\nTTTATATCCGTGCTGCAGCTGTTGCTAGACATATTTATTTAAGACCAAACCTTGGTGTTGGTGCTATTCG\nTAAAATTTATGGTCGTGCTCAAAGGAATGGAACAAGGCCATCACATTCATGCTTAGGATCAGCCTCAATT\nGCTCGAAAGGTCTTACAATCTCTAGAAGCAATGAAACTTGTTACTAAAGATGCAGCAGGTGGACGTAGCT\nTAACTCCTGCAGGTCGAAGGGATATGGATCGAATAGCTGGACAGGTTGTGAACAAAGTTTAAAAATATAT\nTACAGAGTTAATATTAAAAAAAAAAAAAAAAAA\n\n>DQ286050.1 Hydra vulgaris ribosomal protein S9 mRNA, partial cds\nCATGCAATGGTCTTGTTCGTATTGGAGTACTTGATGAAGGAAGAATGAAGCTAGATTATGTTTTAGGTTT\nAAAAGTAGAAGATTTTTTGGAAAGACGTCTACAAACTCAAGTGCTTAAGTTGGGTCTCGCTAAGTCTATT\nCACCATGCTCGTGTTCTTATCCGACAAAAGCATATTAGAGTGCGAAAGCAGTTAGTCAACATCCCATCAT\nTTATCGTGAGACTTGACTCTCAAAAGCACATAGATTTCAGTACTAATTCACCATTCGGTGGTGGTCGACC\nAGGACGTGTTTCACGAAAGAACATGAAGAAAGGTGGCAGTGGAGGAAACGATGAAGAAGACGAAGATGAA\nTAGATTATATTGAAATCTGGCATGTGATTGTTTTGTTAGGCGGTTAATAAAGATCATTTGTCAAATAAAT\nCTAAATACTGTACAATAAAAAAAAAAAAAAAAAAA\n\n>DQ286049.1 Hydra vulgaris ribosomal protein S7 mRNA, partial cds\nACATATGGCTGGGTTCGTGAGCTAGAGAAAAAGTTTTCTGGAAAGCATGTCATTGTTGTTGGACAGAGAA\nGAATCTTGCCTAAACCCAGTCGTAAGACAAGAAATCAAAAGCAAATGAGACCAAGAAGTCGTACTCTAAC\nTGCTGTGCACGATGCCATTCTTGAAGATCTTTGTTTCCCATCGGAAATCGTTGGTAAAAGCATTCGAGTT\nAAATTAGATGGTTCAAGATTGATAAAAATAGTTTTAGAAAAAGCTCAGCAAACAAATGTTGAACATAAAC\nTTGACACGTTTGCAAATGTTTACAAGAAACTAACTGGTAAAGACACTCATTTTACTTTCGAAATATAAGT\nCATAACAGAGAAAAAAAAAAAAAAAAAA\n\n>NM_001309772.1 Hydra vulgaris phospholipid hydroperoxide glutathione peroxidase, mitochondrial-like (LOC100215761), mRNA\nATGGCTGCATCAGACCCTACAAAAGCTTCTTCTATATTTGAATTTCAAGCAAAAAGTATAGATGGTGAAG\nATATCAGTCTTTCGAAATATAAAGGTTTTGTTACACTTATTGTTAACGTGGCTAGCAAGGGTTTAACTGA\nACTCAACTATGCTCAGCTTGCTGATCTGCACACCAAGTATGCTGAGAAAGGTCTTCGAATTCTTGCTTTT\nCCTTGTAATCAGTTTGGTAACCAAGAGCCTGGTACAGATTTAGAAATAAAAGCGTTTGCATTAGCGCGAG\nGCGCCCACTATGACTTATTCAGTAAAATTGATGTTAATGGAGATAAGGCAGATCCTCTGTATAAATATTT\nGAAATCAAAGCAGAAAGGTATTTTGGGTAATAAAATCAAATGGAATTTTTCAAAGTTTATTTGTGATAAA\nAACGGTATCCCTGTTAAAAGATATGCTCCTACAACAGAACCTTTGTCATTAGTTCCAGATATCGAAAAGT\nATTTATGCCAATAA\n\n>NM_001309736.1 Hydra vulgaris superoxide dismutase [Mn], mitochondrial-like (LOC100209764), mRNA\nATGTTTTCTTTTGGAATCCACCGCCTTTCAGTTTTTCGAAAAATATCGAGAATAGCATTTGCTAATAAGC\nACACTCTTCCAGAATTGGGGTATGAATATAATGCATTGGAACCAACAATCAGCAGTCAAATTATGGAGAT\nACATCATCGCAAACACCACCAAGCTTATGTAAATAACTTAAATACAGCAGAAGAACAGTTAGCTGAAGCT\nCAGCATAAAGGAGATACGTCAAAGATTATTTCTTTAGCTCCTGCGTTAAAATTCAATGGAGGTGGGCACA\nTCAATCATTCCATTTTTTGGACTAATCTTTCGCCAAACGGTGGAGGAAAACCAACAGGTGAACTATTAGA\nAGCCATATTAAAAGACTTTGGGTCTTTTGAGGCAATGAAAACACGGTTATCGTCTCCAGCTGTTGCAGTG\nCAAGGTTCGGGTTGGGGTTGGTTGGGATACGATTCTGTCACTAAAAGACTTGCAATTACAGCTTTACCTA\nATCAAGATCCTTTGCAAGCTACTACTGGGTTAATACCGTTACTCGGTATTGATGTTTGGGAGCATGCGTA\nCTACTTGCAGTATAAGAATGTTCGTCTTGATTATGTCAACGCAATATTTAACATCATTGATTGGAAAAAT\nGTATCCGCAAGGTTTGTCGCAGCTAAATAA\n\n'#read a fasta file from your computer
import Bio
from Bio import SeqIO
for seq_record in SeqIO.parse("hv_nt_seq.fasta", "fasta"):
print(seq_record.id)
print(repr(seq_record.seq))
print(len(seq_record))DQ286061.1
Seq('TGTTGTGCTGTTGCTGATCGAACTGGTCATTCACTACTTCATACTCTTTATGGA...CTT', SingleLetterAlphabet())
1212
DQ286057.1
Seq('TGACAACTTTCTGCTGTTGGGCGCCGGAAAGGTAGTGCTTTTCAAACTGTATCA...TTT', SingleLetterAlphabet())
2115
DQ286058.1
Seq('ATTGGTCGTTATTGCGGTCAAGGACGTTACCCATTAATGTCTTCAGTGGGTAAA...AAA', SingleLetterAlphabet())
318
DQ286055.1
Seq('GAAGTTTAGAATTCTTCCAGACTACTTATTAACAGATTATACTGACAGTAGATG...CAG', SingleLetterAlphabet())
750
DQ286054.1
Seq('TTCTTCAATATTTTAATCAACACAGAAAAAAAATATTTTGACTGTAAAAAAGAA...CAA', SingleLetterAlphabet())
574
DQ286051.1
Seq('CAGCTTTAATGGCCCTCAAGAATTTGTAAAAGCTTTTGCTGGACACCTAAAAAA...AAA', SingleLetterAlphabet())
453
DQ286050.1
Seq('CATGCAATGGTCTTGTTCGTATTGGAGTACTTGATGAAGGAAGAATGAAGCTAG...AAA', SingleLetterAlphabet())
455
DQ286049.1
Seq('ACATATGGCTGGGTTCGTGAGCTAGAGAAAAAGTTTTCTGGAAAGCATGTCATT...AAA', SingleLetterAlphabet())
378
NM_001309772.1
Seq('ATGGCTGCATCAGACCCTACAAAAGCTTCTTCTATATTTGAATTTCAAGCAAAA...TAA', SingleLetterAlphabet())
504
NM_001309736.1
Seq('ATGTTTTCTTTTGGAATCCACCGCCTTTCAGTTTTTCGAAAAATATCGAGAATA...TAA', SingleLetterAlphabet())
660from Bio import SeqIO
sizes = [len(rec) for rec in SeqIO.parse("hv_nt_seq.fasta", "fasta")]
sizes[1212, 2115, 318, 750, 574, 453, 455, 378, 504, 660]len(sizes), min(sizes), max(sizes)(10, 318, 2115)