biomaRt/ENSEMBL: Upstream sequences of nicotinic acetylcholine receptor subunits

Libraries

library("biomaRt")
library("Biostrings")

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library(BSgenome)

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Upstream 100 base sequences of nicotinic acetylcholine receptor subunits

ensembl=useMart("ensembl")
hsensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
hsensembl

## Object of class 'Mart':
##   Using the ENSEMBL_MART_ENSEMBL BioMart database
##   Using the hsapiens_gene_ensembl dataset

entrez=c("1134", "1135", "1136", "1137", "1138", "8973", "1139", "55584", "57053",
         "1140", "1141", "1142", "1143", "1144", "1145", "1146")

nachr_coding_gene_flank = getSequence(id = entrez,
                                      type="entrezgene",
                                      seqType="coding_gene_flank",
                                      upstream=100, 
                                      mart=hsensembl) 
str(nachr_coding_gene_flank)

## 'data.frame':    17 obs. of  2 variables:
##  $ coding_gene_flank: chr  "GATTTTGAACCCCTGTATTTTCTTTTCAAAACCCCCTTTTCCAGTGGAAATGCTCTGTTGTTAAAAAGGAAGAAACTGTCTTTCTGAAACTGACATCACG" "GCGGTGTGGGCTCCTTGTGCCCAGATCCTTTGTATTCATAGGGGGAAGTGGAAGACCACGCTGCCTGACTGAGACTTTATTATAGAGGCTCAGGAAAAAG" "CTTCTGATGATGTCAAGGTTGGATGCATGTGGCTGACTGATAGCTCTTTGTTTTCCACAATCCTTTGCCTAGGAAAAAGGAATCCAAGTGTGTTTTAACC" "GGGAGTGTAGGCTGTTATATGACACCCAGAGCCCATCTCTCTCTGCCCCAGACCTTGGAGCTGTTGTCCCACCCCTGTCACTGCAGAGAGCTGAGGCACC" ...
##  $ entrezgene       : int  1142 55584 8973 1146 57053 1139 1144 1140 1138 1137 ...

substr(nachr_coding_gene_flank$coding_gene_flank, 1, 10) # to character string

##  [1] "GATTTTGAAC" "GCGGTGTGGG" "CTTCTGATGA" "GGGAGTGTAG" "TGTCCACACC"
##  [6] "CGCGAGCCGA" "ACCCCCTCCT" "CCAGGAGAGA" "GTCTCACGAC" "ACGTGCTGGG"
## [11] "CTCGCTTTCC" "CTCGGGGGCC" "GGGCGCGGCT" "GAATCCTCAC" "GTCTGGGGTC"
## [16] "CTCCAGCAAC" "AGCCCGGAAC"

subseq(nachr_coding_gene_flank$coding_gene_flank, 1, 10) # returns DNAStringSet

##  [1] "GATTTTGAAC" "GCGGTGTGGG" "CTTCTGATGA" "GGGAGTGTAG" "TGTCCACACC"
##  [6] "CGCGAGCCGA" "ACCCCCTCCT" "CCAGGAGAGA" "GTCTCACGAC" "ACGTGCTGGG"
## [11] "CTCGCTTTCC" "CTCGGGGGCC" "GGGCGCGGCT" "GAATCCTCAC" "GTCTGGGGTC"
## [16] "CTCCAGCAAC" "AGCCCGGAAC"

nachr_unlisted <- unlist(nachr_coding_gene_flank)
nachr_unlisted[2]

##                                                                                     coding_gene_flank2 
## "GCGGTGTGGGCTCCTTGTGCCCAGATCCTTTGTATTCATAGGGGGAAGTGGAAGACCACGCTGCCTGACTGAGACTTTATTATAGAGGCTCAGGAAAAAG"