Here are two lines of code that create data frames using biomaRt's "getBM" function: 

exons7p2 <- getBM(attributes = c("refseq_dna"), filters = "chromosome_name", values = "X", mart = mart.mm)
exons7p3 <- getBM(attributes = c("refseq_dna", "gene_exon_intron"), filters = "chromosome_name", values = "X", mart = mart.mm)

The only thing that differs is that I'm requesting one additional attribute in the second assignment. But if I look at what is in the "refseq_dna" columns of these two data frames, it's completely different. 

head(exons7p2$"refseq_dna") gives a bunch of gene names of the "NM_010498" type

head(exons7p3$"refseq_dna") gives a bunch of sequences

Clearly, there is something fundamental I'm misunderstanding about biomaRt. I would appreciate any guidance. 

Thanks. 

Eric

below is how I made mart.mm and also my sessionInfo()

mart.mm <- useDataset("mmusculus_gene_ensembl", mart = mart.mm)

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] org.Mm.eg.db_3.1.2                      RSQLite_1.0.0                          
 [3] DBI_0.3.1                               TxDb.Mmusculus.UCSC.mm9.knownGene_3.1.2
 [5] GenomicFeatures_1.20.5                  AnnotationDbi_1.30.1                   
 [7] Biobase_2.28.0                          GenomicRanges_1.20.8                   
 [9] GenomeInfoDb_1.4.3                      IRanges_2.2.7                          
[11] S4Vectors_0.6.6                         BiocGenerics_0.14.0                    
[13] biomaRt_2.24.1                         

loaded via a namespace (and not attached):
 [1] XVector_0.8.0           zlibbioc_1.14.0         GenomicAlignments_1.4.1 BiocParallel_1.2.21    
 [5] tools_3.2.2             lambda.r_1.1.7          futile.logger_1.4.1     rtracklayer_1.28.10    
 [9] futile.options_1.0.0    bitops_1.0-6            RCurl_1.95-4.7          Biostrings_2.36.4      
[13] Rsamtools_1.20.4        XML_3.98-1.3           

Dear Eric,

This would be because the "gene_exon_intron" attribute returns the exons + introns of a gene and the "refseq_dna" attribute gives you the RefSeq dna external reference linked to Ensembl Gene IDs. If you have a look on the BioMart interface, you will see that when you ask for a sequence, all the other attributes are in the header (please see: http://www.ensembl.org/biomart/martview?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.sequences.ensembl_gene_id|hsapiens_gene_ensembl.default.sequences.ensembl_transcript_id|hsapiens_gene_ensembl.default.sequences.gene_exon&FILTERS=hsapiens_gene_ensembl.default.filters.chromosome_name."1"&VISIBLEPANEL=resultspanel). I believe this is what is happening here, all the NM_XXXX ids are located in the header of the result but because the sequences are quite big, it's quite hard to see the header.

You can find more information regarding the sequence attributes in the following BiomaRt documentation: http://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/biomaRt.pdf (section 4.7)

All the mart data is linked to Ensembl Gene IDs so it will be easier if you add Ensembl Gene/Transcript/Translation/Exons to your results.

Hope this helps,

Regards,

Thomas

Dear Eric,

I think it will be easier to explain if we look at a particular example, if we look at the Ensembl Gene ID ENSMUSG00000000003 (http://www.ensembl.org/Mus_musculus/Gene/Summary?db=core;g=ENSMUSG00000000003;r=X:77837901-77853623).

Below I am filtering on ENSMUSG00000000003 to only get data mapped to this gene:

> exons7p2 <- getBM(attributes = c("refseq_dna","ensembl_gene_id"), filters = "ensembl_gene_id", values="ENSMUSG00000000003", mart = mart.mm)
> exons7p3 <- getBM(attributes = c("refseq_dna", "gene_exon_intron","ensembl_gene_id"), filters = "ensembl_gene_id", values = "ENSMUSG00000000003", mart = mart.mm)

If we look at the first query, mart return NM_017471 as the value for the "refseq_dna" attribute and you can see that this is mapped to the Ensembl Gene ID  ENSMUSG00000000003.

> exons7p2
  refseq_dna    ensembl_gene_id
1  NM_017471 ENSMUSG00000000003

Now if you add the "gene_exon_intron" attribute in the query you will see that mart will run the above query but it will also fetch the exons + introns sequence for ENSMUSG00000000003.

> exons7p3
  refseq_dna
1 GTCAGTGCACAACTGCCAACTGGGATGCAGAACACTGCTCACGCCAACCATCCTGAAAGCCAACTATAAAAAGCAGAGAGATACTCTGCACCTTTTCAGTGAGGTCCAGATACCCACAGAGCAGAGACAGTCGCTCACACATGATGAGGGTCATCATCCTCCTGCTCACACTGCATGTGCTAGGCGTCTCCAGTGTGATGAGTCTCAAAAAGAAGGTAGCAGACCTGTGTGGAAGGGGGCTGTATGTGGTGGGCATGTTGGGCAGAGACAAACAGACAGAGAGAGGCTTGGGAGGGGGCTTTGTGCAGGTGGGTGGCGACAGCAGGAGACAGGGAGGCAGATGCAGAAAGACTTTAAAGGGGGAAACGAATGTTCTGGAACTTGGTATTTGCTAAGTCTGGTAATAGAGAATAACAAATGTGTTGGGGGGACATAGTTGAGTCTCATAAATGCTTTTCTGAGAGAAAAAGCAGAAGGACAAATACCAAGAGATAGAAACAGAGATAAATGAGAGAGTTCCTGGAGAATTTAACTAGGGATGGACAACTACCCTCTGGAAGTTGCTACTCTTTACATCAGGAATGGAGAGAGACAAAGAAAGAGAGAGTGATCTAAAGGGTGGTTTTCTGAGATAGAGTCACAAAGAAAGGCCAAGAGACAAAGACAGAGAGAATAATGTCTCTGAAGATAGGTTTTTGGTGTGTCTTTGTGTGACAGAGAGAAATGGGAATGGGGAAGAATGTTCTGGAAGTATTCTCTACATCTCAGCATGGAAAGCAGCAGGGAGAGAGAATAGTCTAAATGGTGGTTTTCTGATAGATAGAGACTGAGGACTGAGAGACCAGAGACCTGGAGAACCCGGAGAGAGACATAGAGAGAACATCCATCAGTCTGGAACCAAGGGTGTATCTGACTTTCCCAGAAAATCCAAACACCTACATCACTTCCTATGTTTTCACTCTAGTCCCTCACAAAGCCATGATGACGAATACAATGAAATAATTTTTTTCTCTTTTTTTTATTAGGTATTTTCCTCATTTACATTTCCAATGCTATCCCAAAAGACCCCCATACCCACCCACCCCCAATCCCCTACCCACACACTCCCCCTTTTTGGCCCTGGCCTTCCCCTGTACTGGGGCATATAAAGTTTGCAAGTCCAATGGGCCTCTCTTTCCAGTGATGGCTGACTAGGCCATCTTTTGATACATATGCAGCTAGAGTCAAGAGCTCCGGGGTATTGGTTAGTTCATATTGTTGTTCCACCTATAGGGTTGCAGTTCCCTTTAGCTCCTTGGATACTTTCTCTAGCTCCTCCATTAGGGGCTGTGTGACCCATCCAATAGCTGATTGTGAGCATCAACTTATGTGTTTGCTAGGCCCCAGCATAGTCTCACAAGAGACAGCTATATCTGGGTCCTTTCAGCAAAATCTTGCTAGTGTATGCAATGGTGTCAGCGTTTGGAAGCTGATTATGGGATGGATCCCTGGATACGGCAATCACAAGATGGCCCATCCTTTCGTCACAGCTCCAAATTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTCCCATTTCTAAGAAGGGGCAAAGTGTCCACACTTTGATCTTCCTTCTTCTTGAGTTTCATGCATTTAGCAAATTGTATCTTATATCTTGGGTATCCTAAGTTTCTGGGCTAATATCCACTTATCAGTGAGTACATATTGTGCGAGTTCCTTTGTGATTGTGTTACCTCACTCAGGATGATGCCCTCCAGGTCCATCCATTTGCTTAGGAATTTCATAAATTCATTCTTTTAATAGCTGAGTAGCACTTCATTGTGATAATGTACCACATTTTCTGTATCCATTCCTCTGTTGAGGGGCATCTGGGTTCTTTCCAGCTTCTGGCTATTATAAATAAGGCTGTTATGAACATAGTGGAGCATGAGTCCTTCTTACGGGTTGGGACATCTTCTGGATATATGTCCAGGAGAGGTATTGCTGGATCTTCCGGTAGTACTATGTCCAATTTTCTGAGGAACCGCCAGACTGATTTCCAGAGTGGTTGTACAAGCTTGCAATCCCACCAAAAATGGAGGAGTGTTCCTCTTTCTCCACATCCTCGCCAGCATCTGCTGTCACCTGAATTTTTGATCTTAGCCATTCTGACTGGTGTGAGGTGGAATCTCAGGGTTGTTTTGATTTGCATTTCCCTGATGATTAAGGATGTTGAACATTTTTCAGGTGCTTCTCTGCCATTCGGTATTCCTCAGGTGAGAATTCTTTGTTCAGCTCTGAGCCCCATTTTTTAATGGGCTATTTGATTTTCTGGAGTCCACCTTCTTGAGTTCTTTATATATATATTGGATATTAGTCCCCTATCCGATTTGGAATAGGTAAATATCCTTTCCCAATCTGTTGGTGGTCTTTTTTTATTTTTTTTATTAGGTATTTTCCTCGTTTACATTTTCAATGCTATCCCAAAAGTCCGCCATACCCACCCCCCCAATCCCCTACCCACCCACCCCCCTTTTTGGCCCTGGCGTTCCCCTGTACTGGGGCATATAAAGTTTGCAACTCCAATGGGCCTCTCTTTCCAGTGATAGCCGACTAGGCCATCTTTTAATACATATGCAGCTAGAGTCAAGAGCTCCGGGGTACTGGTTAGTTCATATTGTTGTTCCACCTATAGGGTTGCAGTTCCCTTTAGCTCCTTGGGTAATTTCACTAGCTCCTCCACTGGGGGCCGTGTGACCCATCCAATAGTTGACCGTGAGCATCCACTTATGTGTTTGCTAGGCCCCAGCATAGTCTCACAAGAGACAGCTATATCTGGGTCCTTTCAGCAAAATCTTGCTAGTGTATGCAATGGTGTCAGCGTTTGGAAGCTGATTATGGGATGGATCCCTGCATATGGCAATCACAGATAGTCCATCCTTTTGTCACAGCTCCACATTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTCCCATTTCTAAGAAGGGGCAAAGTGTCTACACTTTGGTCTTCATTCTTCTTGAATTTCATGCGTTTAGCAAATTGTATCTTATATCTTGGGTATCCTAAGTTTCTGGGCTAATATCCACTTATCAGTGAGTACATATTGTGCGAGTTCCTTTGTGATTGTGTTACCTCACTCAGGATGATGCCCTCCAGGTCCATCCATTTGACTAGGAATTTCATAAATTCATTTTTTAATAGCTGAATAGTATTCCATTGTGTAAATGTGCCACATTTTCAGTATCCATTCCTCTGTTGAGGGGCATCTGGTTTCTTTCCAGCTTCTGGCTATTATAAATAAGGCTGCTATGAACACAGTGGAGCATGTGTCCTTCTTGCCGGTTGGGACATCTTCTGGATATATGCCCAGGAGAGGTATTGCAGGATCCTCCAGTAGTACTATGTCCAATTTTCTGAGGAACCGCCAGACTGATTTCCAGAGTGGTTTACAAGCTTGCAATTCCACCAACAATGGAAGAGTGTTCCTCTTTCTCCACATCCTTGCCAGCATCTGCTGTCACCTGAATTTTTGATCTTAGCCATTCTGACTGGTGTGAGGTGGAATCTCAGGGTTGTTTTGATTTGCATTTCCCTGATGATTAAGGATGTTGAACATTTTTCAGGTGCTTCTCAGCCATTCGGTATTCCTCAGGTGAGAATTCTTTGTTCGCCTCTGAGCCCCATTTTTTAATGGGGTTATTTGATTTTCTGGAGTCCACCTTCTTGAGTTCTTTATATATGTTGGATATTAGTCCCCTATCCGATTTGGGAATGGTAAATATCCTTTCCCAATCTGTTGGTGGTCTTTTTGTCTTATTGACAGTGTCTTTTGCCTTGCAGAAGCTTTGCAATTTTATGAGGTCCCATTTATCGATTCTCGATCTTACAGCACAAGCCATTGCTGTTCTATTCAGGAATTTTTCCCCTGTACCCATATCTTCGAGGCTTTTCCCTGTTTTCTCCTCTATAAGTTTCCGTGTCTCTGGTTTTATTTGGAGTTCCTTAATCCACTTAGATTTGACCTTAGTACAAGGAGATAGGAATGGATCAATTTGCATTTTTCTACATGATAACTGCCAGCTGTGCCAGCACCATTTGTTGAAAATGCTGTCTTTTTTCCACTGGATGGTTTTAGCTCCCTTGTCAAAGATCAAGTGACCACAGGTGTGTGGGTTCATCTCTGGGTCTTCAATTCTGTTCCATTGGTCTACTTGTCTGTCACTATACCAGTACCATGCAGGTTTTATCACAATTGCTCTTTAGTACAGCTTTAGATCAGGCATGGTGATTCCATCAGAGGTTCTTTTATCCTTGAGAAGAGTTTTTGCTATCCTAGGTTTTTTGTTATTCCAGATGAATCTGCCAATTGCCCTTTCTAATTCGTTGAAGAATTGAGTTGGAATTTTGATGGGGATTGCATTGAATCTGTAGATTGCTTTTGGCAAGATAGCCATTTTTACTATATTGATCCTGCAAATCCATGAGCATGGGAGATCTTTCCATCTTCTGAGATCTTCTTTAATTTCTTTCTTCAGAGACTTGAAGTTCTTATCATACAGATCTTTCACTTTCTTAAGGGGTGAATTGCACTGACATTATGCTTACAGTGGCAGTTGTCTACTTTGGCCTGTTATCCAAAACATTAAAAGTAAGAACTAAAAAAGATCTGCAGAGAAAGCAAGATGACTTTATTCAAGGCAAAACTAGAGTACAGATTACAGACAGACACACTGCCAAAGATGGGCAGCTGCCCACTTGAGTGACTGGACTCAAGGTCTCCAAGCTATCATGTATGTCTCTATCAGGAGTCCCAAGGAGACCAATAAGCTCGTTACTAAGGTGCCAGATTTATTTTGATTAACAGATTAAAACATTTATTTCTCTAACTGTGTATGCCCCTTCTAGTAATACATCTGATTTTAATCATGCATAGGCCAAATTACACAAAGTCATAATGTGGCCATCTGAAGAACATGTTTTTGTCTTACTATGTAAACACCCCAAACCAGTTCAGGCAAAAATAGTGCTTCTGTTCTCCATACAAGGATACACTGAGAATATAGTTGAATGGAAACTGTCTGGACTTGATCATTATTAGGGTTGTGGGAAGTCAGAGACAGGTGTATGACTAGCTGGATACAGGGTTGGGGACTATGAAGGGTTCTTTTGTGTACTCTACAGCCTTGTTCACAGATGAGTGTGTGAGTATTCTAATACAGGTGGGGAGGAGGAAGAAGGGGTTGTTATATGGAGAACTCTATAGCATTGCTCAGAGAGGGGTGTGTGAGTAACCAGACACAGTTGGCTTGGGGAGGGGTCTAAAATCATGATTGGGTTCATTGAATAGAGTATGCATGAACATAAAAAAAGTTAAGCTGCCTAATGCCTTTTTATATAATCAAGTTGTGAATTATCCTTATCCAAGTGGTTTGGAATTCCCAGTTACTACACTATCCCCTACTTTTAAATGCATTTTTTCAATTGCTGCTTTTTTTCCAGATTGACGGGCCTTGGCAAACAATTTACTTAGCTGCCAGTACCATGGAAAAGATAAATGAAGGCTCACCATTGAGAACCTACTTCCGTCACATTTTGTGTGGGAGGAGATGCAACCAAGTCTACCTCTATTTTTTTATTAAGTAAGATATATATAGACAGAACAATCCATGTGATGGTGTGTGGGTAGAGAAATGAAATGTTTTCAGTCAACACTCATATCAGTGAACACACACAGCACTAAGTGAGGATCCTTGTATCACTTTGCTCTCTGTGGCCCTGAAAAGAACATATGATAGCTGTACTTTTAATTTAGAAAGAGTTAATTTATTTATTTTATAGCAAGCCAAAGTAAAATAAATAATATCAAGAGATGGGTGGTGATTATATGTAGATGATTTATACATAGATAATAGATATAAAATTAGATAGATGATACATATATGACTATGTAGGTGATAGATACATAATTAATAGATATAAAAGTAGATAAATGATACATATACACAAATGTAGGTGTTAGATAATAGACAATTAGCTAGACATGTGATAGATATATACATAGATATGTAGGTAGACAGATAATAGATGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAAAATATATATAGATAAATAATAGATGGATACATGCATGTATATACATAAATATATACATAGGTAGATTTAGATAGTATATAGATATATGAAAGAGACAGGCCTGGGTGTAAAGTACAATTGGAAAACATATTCAAAATCAGCTCCTTGTTGAAGTCAAACATTACAAGACAATTTACCAAAATAACAATTACTTAATTTTCTATTTATCACTGCTCAAAAGCCCAGGTGGTAGAGAAGATATATCAAAATAAATTTTGGGATAGTTTCAGTGCTTTTAAACTATATTGATATGAGTGATATTATCCATCGAGGATATATTTCTATCTGGGAGGAACAAAGTTTTTGTTAATTATGTGCTGATATTTGAACCTTTTCATAAATTAGCTATTTATAAATTCAGGTTTCTGAGAGTCTCTGTACATTGTTCTTGCTTTGAACTCAATATGGAGTAAAAAATAAACTTTTTAATTTTTATTTATTATATACACATATAATAAATAAATTAATAAACATATTGTATTTTTTCTGGACAGTGTTTCTCTGTGTAGCCCTGGCTACCCTGAAACTCACACTGTAGACCAGGCTGGTCTCAAAATCAGAGCCTCTACCTTCTGGGATTAGAGGTGTGTGTCATCACTACCTGGCTAATTTATATATTTTTAAAGACAGGTTCTCCTTATATAACCCTGGCTGTCCTGGAATTCTCTATGTACACCAGACTGGACTTGAACTCACAGAGATCTACCTGCCTCTACCTCTCAGGTGCTGGGTTCAAAAGTGTGTACCACCACAAGCAGTCTTTTTATGTTTTTATTTATTTTTGTTTTTAATTAATTTTTTTTAGAATGATAGTGAACCTATCCTCCTGAATCAGTCTGTTATGGATTCCACCATGCTTGACTTGATATTTAACATACCTAAAATTATTTAAAAGAGTAGTAGTTCAAAATCAAGTAGGTGTATACACTAGAATGTTGAAGAGATAATTTTATTTTTAAATACGTTTTTAAACTAAAACATAATTACATCATTTCCCCCTTCCATTTTCTCCCTCCAATCCTTCCCATGTTCCCTCCTCCCTTGGTCTTTTTCAAATCCTAGACTCCTTTTTCTTTAATTGTTCTCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCGCGTTCTTATTATACAACCTGTTCATTCCATATAATGTTACTTGTATATATATGATTTTTACAGTAACCATTTGATATTCAAAAAACTAACTGAGAGGGAGCACTTTTCTTCAGGGAAGACTACAAAATATCCTAAAATTCAATGGAGCCAGAAAAGATCCTGTGGCAGCTAAAACAATCCTGAGCAAATAGAACAGTGCTGGAAGGATTGCCATTCCAGATATGAGTGATTTTTTTTTACATGCAGAGAATGGACCCCCAAGGCCTTCAACAGGCTTTGTGTAACCACACCCTGCTATTAAACAGTTATTTCCATTTTTTGTTTGTTTTTGGTGGTGTGCTTTTAATGACTGAGTCATCTCTCCAGGCCAGTTATTCTCATGTTTTTAGAGCCATAAAGACAAATCTAAGCTGTGGCTGTCACTATTAGTCACATGGGTCTCTTCTGAGTGAATACAAATCTGAATGCATGACTATGCCTACAACTCTATGGATCTGTTGATGCACATCGCAACTTAAATCTTCTCAGAATACAATTGTAGGCTGAATTTAAATCCATTTAAATGCACAATTCAATTGCTGCTACAGAATCTATAAGATTGATGACATTTATGAGAGGGACAAAAAGTAAATACATGATCCCAATGTAAATATGGATGCTAGACTATAATGTATGTAGGGCACTGAATGTGCTCTGCACCAGGTGGCCTTTCACCCTTTAAACCCAATTCTACAGACATTTCTCATCTCAGATTGGGGTAGAATTTTTGCTCAATATTTTGGATTTTTTTCACTTATCAAAAGTTGTTATTGGGTGCTGGGGATACAGCTGTGTTGGGAGTGATTTAACAGCATGAACCACAGACCCCAGGGCTCCATACTCTGCACAAAGTTCAGTATTACATTCCCATCATCCCAGCACTTGGTGAGTAGAGGCAGGAAGATCAGGGGTTCAAGGACATTCATTGGTCAGAGGTCAGGATAGGCAACAGATCACACAGAGGAGCTAAATCTGCCCTAACAGAGACAACTGCAAACAACTAACAGGGTGATTGATGACTTTTAAGGATGTTATTAATTATATTTAAGGAAAATGCCCTACAACTACATGTGCTTATAAGAGATCTACAGAGGAAAATGTGGTTTGCAATAAACTATCCTGTCATTTATGTGGAATCAGGACCCTGGAGTAATATACAATACGACATTTGTTTTTCAGGAAAGGGACTAAGTGCCAACTGTATAAAGTCATAGGAAGGAAAAAACAAGAAGTTTACTATGCACAGTGTGAGTAAGCAATGCCGGAATGAATGCACGACCTTAATTGTTTCTTTTTTCAAAATTCACTGTCTTGGTTGAATTTTGCACACCTTGATATCTACATTCCAATGTAATTGTCTCTACAAATTACAGATGCAATCTTGAGGAAAGCCTCCTCATTTTCTTCCTAGTCATTTTGGAACTAATAAGAGATTTAATTTGTTTGTTTAGTCTTTAATGACTTTTAAAAACTTTTTTATTTATATGGTGTATACCTCTACCAAGCACACTTCCCTGGTTTAGCTTTACGGGTAAACTAAATCACAGACAAGAGTCTGAGAATGGTTAAAAGAATTAAAAGGTGATTTGAGCACTTTAAAAAATAACGATGCAAAATAGGAACTAGGATTTTATCAACTATGAAAATGACTCCCAGCAATTCTGAAACATGTGTCTTGTACAAGGAATGATTAATTGTCTAAATTTTATAATTTTATTGGGGAAAATGATTTACAATATATAAAATTAAGCATCATGAATAGTCTTAGCTCTTTAGTTCTGAAAGGCAAGGTATATGACATACTGAGATCCATTTATAAATAATTCAGGTATCAATTTAATTTGTCATGAATCAAGTGGTAAAGATACTTTCATTATTTTCTATTCTACCATAAAGAGTCTATTTAACGCAATACATTAAACTGATAAACTAAACATGTCATGGACTCTAGGTTGGTTTATAGATAAGTTTATAGAAGAGTTTATTGTACTTAAATAGAGGAGCCGAATCAACTCACAAGTATATATCCCTCCAAAAAGCCCCACACACACCTCCTAGTGTGTTATGTAATTTAGTTGGAGGCCAGCCTGATCTAAACAACAAGTTTCAGGCCAGCCAAGGATACATAGTAAGACCCGTCTCAGAAGGAAAAGGAGTTACCACTGACATAAAAAGGAACAGTCATCATATCAATGAGGAGGATCTTGAGTCAACCCCTTCCCCTCTTTAAGAAGTCTTGCTAGTGAAGCAGTGAGTGTATTGGAGTCACATACAAGAACATTTGGAAATATGGCTGCATTCCTGAAAAGCCCAACTCAGCTTGGATGACACTCCTGAAAGTTTTATCCTTGGAGCTTTAGCAAGGCTTACAGACAGCTAAGCTAGTCAGAGTCTCTTCTAGAGGGCTTGTTCACTGTTTCCCATAACGTTGTGGAGGGGCCTACTGAAAGCTGTTGGTCTCAAAATCATCCTGAGATTTGTGGGGTTTTTACTTCTTGAATCTCATGAGCTACTAAGACAGAATGTTCCAGTTTGGAGAAAATCACTATGTGGCACCCTCCCTTTTTTCTGACATGCCTCTGAGGAAAATTGGTAAAGTTAGATAATTGCACCACTAAATGTAGATCAGCTCCATGAAAATGTTGAGATATATATATATATATATATATATGTATATAAAATCAGAGAGTTTTCCTCAATATGTGTATATATGTGTATATAATTCCACCATTAAATGTATTAAATGTATTAGGATCCATGAAAATGCCTATATATGTGCACACACACTATATATATATATATATATATATATATATATATATATATAATCTTTCCTCAATATATGTACTATAAACAATTCCACCATTAAATTTAATAGGATCAATGAAATGTATGCACATATTGCATATACATATAATCATACAGCTATTCTCAGCAAGTAAGAGGACTGCAGTATGTCAGCTTCTATACATTCACACATCTTGGTATCAAGAACATAGCTATTCCAAACCAATATAGGTTCTACATATTTGTAGGTAACTGTGGGATGTTAGATATATTTTATATCTTACAACAGAATTATAAACTTGCTTTATAATTCCCTGTTTGTCTTGACTAGTTTCAACACATGGAGCAGAATATTGTAGGTTAGGGACTGTATACTCCATATATACATTCATAACTGTGCAGGTAGAATGAGTCTGAGCAAGCATTTTGTTGACTTTATATGTATTTATACAAATGTCTTACCTATCTCAGATGAAGGGAGCATAGCATTCATGTTAAAGATGGTAAATGAGAAGATATTGTTGTTTCATTATTTTAACAAGAACAGAAGAAATGATGTCACACGAGTGGCTGGAGTTTTGGGTAAGTGTCACACATAGAACTTGTAATGTGAGAGTGTGATTCAAGGATATGAATGTATGCATATCTCTGTACCCAAAGATCACAATGTGTTTGTGTATCTGATTCTGTATGTCAGGTTGATAAATCACTGAAGCTGTCATAGTTAGCTTTGAAGATCAACTTGGAACAACCCAGAATGCCCTGGGAAGGGTCTCAGTAGGGAGATTAAGCAACAGAAATATTTTATTAGTGTGCTGGGTACTAATGTTGTGACATATTCCCTATACACCGTGAAACGCAGCAAAAGGCAAACAACTGAATAAGGAGGAGATGACGGAGTTCATGAACTTAGTGGAAGAAATGGGCATTGAGGAAGAGAATGTACAGCGTATCATGGACACGGGTATAGTAGCAACCTACGTGTGTAACTTCTTACTTTGTATTTTTATAATAAATGTTATTTTTTTATTATTGAGGGTGTTGGGAAGTTGGCTCAGTGGGAAAAGTGCACACAAGCATGAGGGCCCAAGTTTGGATCCCAGCACCCATTTAGAAAGCCAAGAATAACAGAGCTGGAAAGGGGAGGGGACAAGAGGAGCTCTCTAGTAATAAATCTATCTGAAAGGTCATATTTCAAAACTAACAATGTGTAGAATGATTAAAGGAGGTGTTAAAAAGTCAGCCTCTTACCTATGCATGCGTGGGCATACACATGTCATTCACACGACTATGAACACACCAATAAACCATGCAGATAGAAACACACACACACAAAATCTACCTGAAATGAAACTCAGTTCCTAGGTCCCTCTGTCCAGATACTCTAGTCAAAACCTAGCTTTATATCTGCATTTTTATGAAAACTGTTCATATGTACTAATGTTATTACTAATATTATGTTGAAGTACTTTATTACTTTAAAATAATACTGTTGTTTTAAAATAATACTTTACTTTAAATGTTAGTATGTTAAAAATAATATATTTCCGTGTTTACTCTCCTTTAGACAACTGTCCAAGCAAGATCAAACCTTAGTGACTCAACAAGATCAGGATTAGGTGAGTCAAAGCACATTAATTTTATATCTTGAAGTTTTAATTTTAATTTTATTTTAATATTTAAGTTATTAATATTTAATATTTAAAGTAAATAATATTTTATTTGTTCTTTATCCTTTTCATATATTTATATAATGTATATTTATCTTTCATACTTCCACACACCTCATCCAAGCAACACATCTCCCTCTATACTTCATGGCTTTTAAATTTTATTATTATTTATTATTATTATTACCTCAATGAATCCAATTGGTGCTATTTCTGAATAGGGTATGTCAATTCCTGGAGGCATGAGTAATGTAATATACCAGGGCTATTATGTAATATAAAAAAATGGACTGCAGGGAGCTGGTGGCACATGCATTTAACCTAGCGCTCAAGAGGCAGAAGCAAGCATATGTCTGCGTTTTAGATAACCCTAGTCTACAGAGTGAGTTCCAGGACAGCAAGGGCTACTCAGAGAAACCCTGTCTCATAAAACCAAAAAGTATATTTTTTAAAGGCAGAAGAGGAAAGGAGGGAGGGAGGGAGGGAAAGAGGCAGACAGACAGACAGGCAGGCAGGCAGGCAAAAAGAAGGAAAAAGAAAAATATGGACCCTCCCTCTCCCAGAAACTATCAACTGGCAATAGCTCTTTGGTGGGGGGGGGGGGTCCTGAATCCCTCTCTGCTCAATTCTAGAATGTTAATTAGCTTGATCTGACCAGGGTCTTGTGCAGAACACCACAGTTGCTGTGAGTTCATGATTGTAACAGATCTGTCATGTTCAGAAAACAGAATTTTATGGCTCTACTCCCCATCCAGATGATAATTGATGGCTAAGCATCCACAGTCACTTGTCCTCATCCTTTGACCAGCTACAAATTTCTGCACAAACCACTCCCCACTGTAAAAAGTTGAGCAGAAGTCAAACATGGAGGCACACACCCTTAATCCCAACACTTGGGAGGCACGGGTAGATGAATCTCTGTGAGTATCAAGCCAGCCTGATCTACATACTGAGCTCCAGAAGATCCAGGTACATAGTCTCTATCTAAACAAACAAACACAAAGTTAAAAAGTTGATTTGACCAAAATTGAGAGAAGCATAAATCTATGAGTATTTTTAAGACCGTGGCTTGGAAACATGACAGTTCATCACCACTGGTCTCCTTCATAGGCTCCATGAGCTCCATTGTCACAGGCTTTTGACTCGAATTACAATAGAAACCCACCCTTACCCCTGTTCTTCCATAGATATGAAGTTCCTTCCATGGAGCTGGCATGAAATTTAATCAGAGAGTGCTTGGCTCCCCAATACAGCCTTTATTGCACCAGTGGACGCAAGGATGATTTTATAGTGTGTTGGGGAAGCATGGTGACATCACTGACATCTTATCCCACATACACAGCCTATTAAGTACATCTAAGCACTGTGAACGAGTTTCCTAGTCCATTTGACATCGATTTCTTGATGCCCTACAGCCACAGCATTTGGTGTCTTCAGCAATAGTGCCCTACCATTTAGATATGGTGTATAGTCAAGAGATATGGCAATAGCCAAGTTATTTTGGTTATTCCAAGGCTTCCTTCCATTAATAAATATCATGGTGGTACCCCCATGACTAAAAATTAGATTTTCACTGAATAAACCATGTCTTCTGGGAACAGCATTATACCATTGCAGGGATCCTCTGCTGAAACTTTTTTAATACTATATTTTTACTTAGCTTACAAACTAGTGGATTTCTGTAAGACTTCATTTACCTTCAGTTTCAGTTGACCCTCCCCTACCCTGTTCTTCCCTATGCCCAAACACATCCACACCTACTCCTCTAGCCCACAGCTCTCACTTTCTAATCTTCCCTGTCACCAGTGCCCAATTATATCGCCTGTATTATTATATTTTAATCACACAACCATAGGTTTCCATATGAGGTTTTAATAACCCTTCATTCTGGTTAAACCTTCCACCACACCCTGATTTCCCCATTCCACAACCAACTCCATGATTAAGCCTTCCTGCCCCAAGTATTCTTCTTTATACTTCATTTTAATGGCATTACATTTGATGGACCCACTTCCTTGATGGACCCAATTCAAACCAGTTTCTAATTACCTGGATTCCTTACATACTCCATATTATGCATACAAAATAAAAGATTCAAGTCTAATGTCCACATGTGAGATAGAATGTGCAGTTTGTCTTTCTGAGCCTGAGTGGCCTCATTAAGTATAATAATTTCCAGTTCCTTCTATTTACTTGGAAATTTCATATTTTCATTGTTCTCTATGGCTGAGTAATATTCCATCTTATACATTACATTTTCCTTATCCATTCATTAGTTGATGAACAGTTGGGTCAACTTCGTTTCTTAGCTATTATGAACTTAACCTCAGTGAGCATGGACATTCAAAGGTCTCTGTAACAGAATATAAACCCCTTTGTGTACATATCTAGAAATGGAGGAACTAGAGAAAGCACCCAAGGAACTAAAGGGAACTGCAACCCTATAGGTGGAACAACAATATGAACTAAGCAGTACCCCGGAGCTCTTGTCTCTAGCTGCATATCTATCAAAAGATGGCCTAGTCGGCCATCACTGCAAAGAGAGGCCCATTGGACTTGCAAACTTTATATGCCCCAGTACAGGGGAATGCCAGGGCCAAAAAGGGGGGATGGGTGGGTAGGGGAGTGGGGGGGGGTTGGGGACTTTTTGTATAGCATTGGAAATGTAAATGAGCTAAATACCTAATAAAAAATGGAAAAAAAAAGAAATGGTGTAACTGAGTCACATGGGAAGTCTTTTTCTAATCTTTGGATTTGTTTATTTGATGTTCATAGTTTTTGGGTTTTGGTTGGTTTTGTTCTAAGTTCTTTGTATATTGTAGACACTAATCCTCCATCACATGTGTAGTTGGCAAAGATCTCCATTCCCCGAGATACCTGTGCATTTAATTGACAGCTTCCTTTGCCGTAGTTTTTAATTCCATGATATCTGACAAGTGTTTGTCTTACTTTCTTGCTACAAGAATCCTATTCAAAGAATCCATACCTGTGTCTATGGTTAACACACACTCCATGCTTTCTTCTCTATCAGCTTCAGGTTACCATGTCTTATGACACGGTCTTTGAATCATTTGGAGTTGAGGTTTTTTTCAAGGTGACAGGGAAGAGCCCAGGTTCATTTCTCTGTATCCTGATGTCCACTTTTTCCTATTCGGTCTATTTATGGAATTATATATTTTTATGTTAGGTCATTTTTCAGTGGAGGCATTAACAATATCCAGAAGGGGACTATTTCTTACTAGTGTTGAGATGGTATTCTCCTATATGGGGCTGGTACTGAAGGCAGCAAGTTCTACCCCTAGTCTTCCTGTGAGATTCAACTACTATCTGGGACCTCGAGTGAGACTCTGTCTGTAGGATACATGGGGCTTGGTAAACTCCAATGTGAAACAAAAAATATATAATTTTAGTTTAGATTCATAGAAACTACATCCTCAAATAAACACATAAGTTCTAAAAAGTACCAATTTAGGTCTTGATATAAGATCATTTGTCATATAAAAATTTTCCATATAAGGAAAATTTCCATACAAAGTTCATGTATATTTCCAAATATACAAAATTCTGTAAAATGTTTTTGCATGATACATCTTGTCATTGTTTGCCTCTTTAATGGCTTGTATTTGTTTCATTTTCTACTCTCATCAAATATCATGTATTACTATCCTAAATATATGAAATAATTCTGTTCCAGCATTACAGATGACATCAGGAATTTTCCAGTATATTTTTCCTGGAACCTGAAACATCAATATGAAGATGAAGCAATCTTGTCTCTCAGATCATATTTTCCTATTTATTGCAAATTACAATTCCTGTCTCTGTACTTTCTCTTTCACTCATTGTTTCCCATGTTCTAATCGGTATTAGTGCATCTTTGAATGTTTAAATAAATTTATTTTACTTGC
  gene_exon_intron    ensembl_gene_id
1        NM_017471 ENSMUSG00000000003

Because the sequence is so big and BiomaRt display the header after the sequence then it can be a bit hard to spot. You are right, something is not right here as the "gene_exon_intron" and "refseq_dna" headers seems to be inverted in the second dataset. I will report this to the BiomaRt main developer.

Hope this helps,

Regards,

Thomas

Dear Eric,

This is indeed down to the fact that the BioMart website interface does not allow joins between sequences and external references and the BiomaRt package allow them. There is a setting that you can turn on in your query to get the BioMart website headers instead of the BiomaRt package headers called "bmHeader=TRUE", please see example below:

> exons7p3 <- getBM(attributes = c("refseq_dna", "gene_exon_intron","ensembl_gene_id"), filters = "ensembl_gene_id", values = "ENSMUSG00000000003", mart = mart.mm, bmHeader=TRUE)
> exons7p3
    Unspliced (Gene)
1 GTCAGTGCACAACTGCCAACTGGGATGCAGAACACTGCTCACGCCAACCATCCTGAAAGCCAACTATAAAAAGCAGAGAGATACTCTGCACCTTTTCAGTGAGGTCCAGATACCCACAGAGCAGAGACAGTCGCTCACACATGATGAGGGTCATCATCCTCCTGCTCACACTGCATGTGCTAGGCGTCTCCAGTGTGATGAGTCTCAAAAAGAAGGTAGCAGACCTGTGTGGAAGGGGGCTGTATGTGGTGGGCATGTTGGGCAGAGACAAACAGACAGAGAGAGGCTTGGGAGGGGGCTTTGTGCAGGTGGGTGGCGACAGCAGGAGACAGGGAGGCAGATGCAGAAAGACTTTAAAGGGGGAAACGAATGTTCTGGAACTTGGTATTTGCTAAGTCTGGTAATAGAGAATAACAAATGTGTTGGGGGGACATAGTTGAGTCTCATAAATGCTTTTCTGAGAGAAAAAGCAGAAGGACAAATACCAAGAGATAGAAACAGAGATAAATGAGAGAGTTCCTGGAGAATTTAACTAGGGATGGACAACTACCCTCTGGAAGTTGCTACTCTTTACATCAGGAATGGAGAGAGACAAAGAAAGAGAGAGTGATCTAAAGGGTGGTTTTCTGAGATAGAGTCACAAAGAAAGGCCAAGAGACAAAGACAGAGAGAATAATGTCTCTGAAGATAGGTTTTTGGTGTGTCTTTGTGTGACAGAGAGAAATGGGAATGGGGAAGAATGTTCTGGAAGTATTCTCTACATCTCAGCATGGAAAGCAGCAGGGAGAGAGAATAGTCTAAATGGTGGTTTTCTGATAGATAGAGACTGAGGACTGAGAGACCAGAGACCTGGAGAACCCGGAGAGAGACATAGAGAGAACATCCATCAGTCTGGAACCAAGGGTGTATCTGACTTTCCCAGAAAATCCAAACACCTACATCACTTCCTATGTTTTCACTCTAGTCCCTCACAAAGCCATGATGACGAATACAATGAAATAATTTTTTTCTCTTTTTTTTATTAGGTATTTTCCTCATTTACATTTCCAATGCTATCCCAAAAGACCCCCATACCCACCCACCCCCAATCCCCTACCCACACACTCCCCCTTTTTGGCCCTGGCCTTCCCCTGTACTGGGGCATATAAAGTTTGCAAGTCCAATGGGCCTCTCTTTCCAGTGATGGCTGACTAGGCCATCTTTTGATACATATGCAGCTAGAGTCAAGAGCTCCGGGGTATTGGTTAGTTCATATTGTTGTTCCACCTATAGGGTTGCAGTTCCCTTTAGCTCCTTGGATACTTTCTCTAGCTCCTCCATTAGGGGCTGTGTGACCCATCCAATAGCTGATTGTGAGCATCAACTTATGTGTTTGCTAGGCCCCAGCATAGTCTCACAAGAGACAGCTATATCTGGGTCCTTTCAGCAAAATCTTGCTAGTGTATGCAATGGTGTCAGCGTTTGGAAGCTGATTATGGGATGGATCCCTGGATACGGCAATCACAAGATGGCCCATCCTTTCGTCACAGCTCCAAATTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTCCCATTTCTAAGAAGGGGCAAAGTGTCCACACTTTGATCTTCCTTCTTCTTGAGTTTCATGCATTTAGCAAATTGTATCTTATATCTTGGGTATCCTAAGTTTCTGGGCTAATATCCACTTATCAGTGAGTACATATTGTGCGAGTTCCTTTGTGATTGTGTTACCTCACTCAGGATGATGCCCTCCAGGTCCATCCATTTGCTTAGGAATTTCATAAATTCATTCTTTTAATAGCTGAGTAGCACTTCATTGTGATAATGTACCACATTTTCTGTATCCATTCCTCTGTTGAGGGGCATCTGGGTTCTTTCCAGCTTCTGGCTATTATAAATAAGGCTGTTATGAACATAGTGGAGCATGAGTCCTTCTTACGGGTTGGGACATCTTCTGGATATATGTCCAGGAGAGGTATTGCTGGATCTTCCGGTAGTACTATGTCCAATTTTCTGAGGAACCGCCAGACTGATTTCCAGAGTGGTTGTACAAGCTTGCAATCCCACCAAAAATGGAGGAGTGTTCCTCTTTCTCCACATCCTCGCCAGCATCTGCTGTCACCTGAATTTTTGATCTTAGCCATTCTGACTGGTGTGAGGTGGAATCTCAGGGTTGTTTTGATTTGCATTTCCCTGATGATTAAGGATGTTGAACATTTTTCAGGTGCTTCTCTGCCATTCGGTATTCCTCAGGTGAGAATTCTTTGTTCAGCTCTGAGCCCCATTTTTTAATGGGCTATTTGATTTTCTGGAGTCCACCTTCTTGAGTTCTTTATATATATATTGGATATTAGTCCCCTATCCGATTTGGAATAGGTAAATATCCTTTCCCAATCTGTTGGTGGTCTTTTTTTATTTTTTTTATTAGGTATTTTCCTCGTTTACATTTTCAATGCTATCCCAAAAGTCCGCCATACCCACCCCCCCAATCCCCTACCCACCCACCCCCCTTTTTGGCCCTGGCGTTCCCCTGTACTGGGGCATATAAAGTTTGCAACTCCAATGGGCCTCTCTTTCCAGTGATAGCCGACTAGGCCATCTTTTAATACATATGCAGCTAGAGTCAAGAGCTCCGGGGTACTGGTTAGTTCATATTGTTGTTCCACCTATAGGGTTGCAGTTCCCTTTAGCTCCTTGGGTAATTTCACTAGCTCCTCCACTGGGGGCCGTGTGACCCATCCAATAGTTGACCGTGAGCATCCACTTATGTGTTTGCTAGGCCCCAGCATAGTCTCACAAGAGACAGCTATATCTGGGTCCTTTCAGCAAAATCTTGCTAGTGTATGCAATGGTGTCAGCGTTTGGAAGCTGATTATGGGATGGATCCCTGCATATGGCAATCACAGATAGTCCATCCTTTTGTCACAGCTCCACATTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTCCCATTTCTAAGAAGGGGCAAAGTGTCTACACTTTGGTCTTCATTCTTCTTGAATTTCATGCGTTTAGCAAATTGTATCTTATATCTTGGGTATCCTAAGTTTCTGGGCTAATATCCACTTATCAGTGAGTACATATTGTGCGAGTTCCTTTGTGATTGTGTTACCTCACTCAGGATGATGCCCTCCAGGTCCATCCATTTGACTAGGAATTTCATAAATTCATTTTTTAATAGCTGAATAGTATTCCATTGTGTAAATGTGCCACATTTTCAGTATCCATTCCTCTGTTGAGGGGCATCTGGTTTCTTTCCAGCTTCTGGCTATTATAAATAAGGCTGCTATGAACACAGTGGAGCATGTGTCCTTCTTGCCGGTTGGGACATCTTCTGGATATATGCCCAGGAGAGGTATTGCAGGATCCTCCAGTAGTACTATGTCCAATTTTCTGAGGAACCGCCAGACTGATTTCCAGAGTGGTTTACAAGCTTGCAATTCCACCAACAATGGAAGAGTGTTCCTCTTTCTCCACATCCTTGCCAGCATCTGCTGTCACCTGAATTTTTGATCTTAGCCATTCTGACTGGTGTGAGGTGGAATCTCAGGGTTGTTTTGATTTGCATTTCCCTGATGATTAAGGATGTTGAACATTTTTCAGGTGCTTCTCAGCCATTCGGTATTCCTCAGGTGAGAATTCTTTGTTCGCCTCTGAGCCCCATTTTTTAATGGGGTTATTTGATTTTCTGGAGTCCACCTTCTTGAGTTCTTTATATATGTTGGATATTAGTCCCCTATCCGATTTGGGAATGGTAAATATCCTTTCCCAATCTGTTGGTGGTCTTTTTGTCTTATTGACAGTGTCTTTTGCCTTGCAGAAGCTTTGCAATTTTATGAGGTCCCATTTATCGATTCTCGATCTTACAGCACAAGCCATTGCTGTTCTATTCAGGAATTTTTCCCCTGTACCCATATCTTCGAGGCTTTTCCCTGTTTTCTCCTCTATAAGTTTCCGTGTCTCTGGTTTTATTTGGAGTTCCTTAATCCACTTAGATTTGACCTTAGTACAAGGAGATAGGAATGGATCAATTTGCATTTTTCTACATGATAACTGCCAGCTGTGCCAGCACCATTTGTTGAAAATGCTGTCTTTTTTCCACTGGATGGTTTTAGCTCCCTTGTCAAAGATCAAGTGACCACAGGTGTGTGGGTTCATCTCTGGGTCTTCAATTCTGTTCCATTGGTCTACTTGTCTGTCACTATACCAGTACCATGCAGGTTTTATCACAATTGCTCTTTAGTACAGCTTTAGATCAGGCATGGTGATTCCATCAGAGGTTCTTTTATCCTTGAGAAGAGTTTTTGCTATCCTAGGTTTTTTGTTATTCCAGATGAATCTGCCAATTGCCCTTTCTAATTCGTTGAAGAATTGAGTTGGAATTTTGATGGGGATTGCATTGAATCTGTAGATTGCTTTTGGCAAGATAGCCATTTTTACTATATTGATCCTGCAAATCCATGAGCATGGGAGATCTTTCCATCTTCTGAGATCTTCTTTAATTTCTTTCTTCAGAGACTTGAAGTTCTTATCATACAGATCTTTCACTTTCTTAAGGGGTGAATTGCACTGACATTATGCTTACAGTGGCAGTTGTCTACTTTGGCCTGTTATCCAAAACATTAAAAGTAAGAACTAAAAAAGATCTGCAGAGAAAGCAAGATGACTTTATTCAAGGCAAAACTAGAGTACAGATTACAGACAGACACACTGCCAAAGATGGGCAGCTGCCCACTTGAGTGACTGGACTCAAGGTCTCCAAGCTATCATGTATGTCTCTATCAGGAGTCCCAAGGAGACCAATAAGCTCGTTACTAAGGTGCCAGATTTATTTTGATTAACAGATTAAAACATTTATTTCTCTAACTGTGTATGCCCCTTCTAGTAATACATCTGATTTTAATCATGCATAGGCCAAATTACACAAAGTCATAATGTGGCCATCTGAAGAACATGTTTTTGTCTTACTATGTAAACACCCCAAACCAGTTCAGGCAAAAATAGTGCTTCTGTTCTCCATACAAGGATACACTGAGAATATAGTTGAATGGAAACTGTCTGGACTTGATCATTATTAGGGTTGTGGGAAGTCAGAGACAGGTGTATGACTAGCTGGATACAGGGTTGGGGACTATGAAGGGTTCTTTTGTGTACTCTACAGCCTTGTTCACAGATGAGTGTGTGAGTATTCTAATACAGGTGGGGAGGAGGAAGAAGGGGTTGTTATATGGAGAACTCTATAGCATTGCTCAGAGAGGGGTGTGTGAGTAACCAGACACAGTTGGCTTGGGGAGGGGTCTAAAATCATGATTGGGTTCATTGAATAGAGTATGCATGAACATAAAAAAAGTTAAGCTGCCTAATGCCTTTTTATATAATCAAGTTGTGAATTATCCTTATCCAAGTGGTTTGGAATTCCCAGTTACTACACTATCCCCTACTTTTAAATGCATTTTTTCAATTGCTGCTTTTTTTCCAGATTGACGGGCCTTGGCAAACAATTTACTTAGCTGCCAGTACCATGGAAAAGATAAATGAAGGCTCACCATTGAGAACCTACTTCCGTCACATTTTGTGTGGGAGGAGATGCAACCAAGTCTACCTCTATTTTTTTATTAAGTAAGATATATATAGACAGAACAATCCATGTGATGGTGTGTGGGTAGAGAAATGAAATGTTTTCAGTCAACACTCATATCAGTGAACACACACAGCACTAAGTGAGGATCCTTGTATCACTTTGCTCTCTGTGGCCCTGAAAAGAACATATGATAGCTGTACTTTTAATTTAGAAAGAGTTAATTTATTTATTTTATAGCAAGCCAAAGTAAAATAAATAATATCAAGAGATGGGTGGTGATTATATGTAGATGATTTATACATAGATAATAGATATAAAATTAGATAGATGATACATATATGACTATGTAGGTGATAGATACATAATTAATAGATATAAAAGTAGATAAATGATACATATACACAAATGTAGGTGTTAGATAATAGACAATTAGCTAGACATGTGATAGATATATACATAGATATGTAGGTAGACAGATAATAGATGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGAAAATATATATAGATAAATAATAGATGGATACATGCATGTATATACATAAATATATACATAGGTAGATTTAGATAGTATATAGATATATGAAAGAGACAGGCCTGGGTGTAAAGTACAATTGGAAAACATATTCAAAATCAGCTCCTTGTTGAAGTCAAACATTACAAGACAATTTACCAAAATAACAATTACTTAATTTTCTATTTATCACTGCTCAAAAGCCCAGGTGGTAGAGAAGATATATCAAAATAAATTTTGGGATAGTTTCAGTGCTTTTAAACTATATTGATATGAGTGATATTATCCATCGAGGATATATTTCTATCTGGGAGGAACAAAGTTTTTGTTAATTATGTGCTGATATTTGAACCTTTTCATAAATTAGCTATTTATAAATTCAGGTTTCTGAGAGTCTCTGTACATTGTTCTTGCTTTGAACTCAATATGGAGTAAAAAATAAACTTTTTAATTTTTATTTATTATATACACATATAATAAATAAATTAATAAACATATTGTATTTTTTCTGGACAGTGTTTCTCTGTGTAGCCCTGGCTACCCTGAAACTCACACTGTAGACCAGGCTGGTCTCAAAATCAGAGCCTCTACCTTCTGGGATTAGAGGTGTGTGTCATCACTACCTGGCTAATTTATATATTTTTAAAGACAGGTTCTCCTTATATAACCCTGGCTGTCCTGGAATTCTCTATGTACACCAGACTGGACTTGAACTCACAGAGATCTACCTGCCTCTACCTCTCAGGTGCTGGGTTCAAAAGTGTGTACCACCACAAGCAGTCTTTTTATGTTTTTATTTATTTTTGTTTTTAATTAATTTTTTTTAGAATGATAGTGAACCTATCCTCCTGAATCAGTCTGTTATGGATTCCACCATGCTTGACTTGATATTTAACATACCTAAAATTATTTAAAAGAGTAGTAGTTCAAAATCAAGTAGGTGTATACACTAGAATGTTGAAGAGATAATTTTATTTTTAAATACGTTTTTAAACTAAAACATAATTACATCATTTCCCCCTTCCATTTTCTCCCTCCAATCCTTCCCATGTTCCCTCCTCCCTTGGTCTTTTTCAAATCCTAGACTCCTTTTTCTTTAATTGTTCTCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCGCGCGCGTTCTTATTATACAACCTGTTCATTCCATATAATGTTACTTGTATATATATGATTTTTACAGTAACCATTTGATATTCAAAAAACTAACTGAGAGGGAGCACTTTTCTTCAGGGAAGACTACAAAATATCCTAAAATTCAATGGAGCCAGAAAAGATCCTGTGGCAGCTAAAACAATCCTGAGCAAATAGAACAGTGCTGGAAGGATTGCCATTCCAGATATGAGTGATTTTTTTTTACATGCAGAGAATGGACCCCCAAGGCCTTCAACAGGCTTTGTGTAACCACACCCTGCTATTAAACAGTTATTTCCATTTTTTGTTTGTTTTTGGTGGTGTGCTTTTAATGACTGAGTCATCTCTCCAGGCCAGTTATTCTCATGTTTTTAGAGCCATAAAGACAAATCTAAGCTGTGGCTGTCACTATTAGTCACATGGGTCTCTTCTGAGTGAATACAAATCTGAATGCATGACTATGCCTACAACTCTATGGATCTGTTGATGCACATCGCAACTTAAATCTTCTCAGAATACAATTGTAGGCTGAATTTAAATCCATTTAAATGCACAATTCAATTGCTGCTACAGAATCTATAAGATTGATGACATTTATGAGAGGGACAAAAAGTAAATACATGATCCCAATGTAAATATGGATGCTAGACTATAATGTATGTAGGGCACTGAATGTGCTCTGCACCAGGTGGCCTTTCACCCTTTAAACCCAATTCTACAGACATTTCTCATCTCAGATTGGGGTAGAATTTTTGCTCAATATTTTGGATTTTTTTCACTTATCAAAAGTTGTTATTGGGTGCTGGGGATACAGCTGTGTTGGGAGTGATTTAACAGCATGAACCACAGACCCCAGGGCTCCATACTCTGCACAAAGTTCAGTATTACATTCCCATCATCCCAGCACTTGGTGAGTAGAGGCAGGAAGATCAGGGGTTCAAGGACATTCATTGGTCAGAGGTCAGGATAGGCAACAGATCACACAGAGGAGCTAAATCTGCCCTAACAGAGACAACTGCAAACAACTAACAGGGTGATTGATGACTTTTAAGGATGTTATTAATTATATTTAAGGAAAATGCCCTACAACTACATGTGCTTATAAGAGATCTACAGAGGAAAATGTGGTTTGCAATAAACTATCCTGTCATTTATGTGGAATCAGGACCCTGGAGTAATATACAATACGACATTTGTTTTTCAGGAAAGGGACTAAGTGCCAACTGTATAAAGTCATAGGAAGGAAAAAACAAGAAGTTTACTATGCACAGTGTGAGTAAGCAATGCCGGAATGAATGCACGACCTTAATTGTTTCTTTTTTCAAAATTCACTGTCTTGGTTGAATTTTGCACACCTTGATATCTACATTCCAATGTAATTGTCTCTACAAATTACAGATGCAATCTTGAGGAAAGCCTCCTCATTTTCTTCCTAGTCATTTTGGAACTAATAAGAGATTTAATTTGTTTGTTTAGTCTTTAATGACTTTTAAAAACTTTTTTATTTATATGGTGTATACCTCTACCAAGCACACTTCCCTGGTTTAGCTTTACGGGTAAACTAAATCACAGACAAGAGTCTGAGAATGGTTAAAAGAATTAAAAGGTGATTTGAGCACTTTAAAAAATAACGATGCAAAATAGGAACTAGGATTTTATCAACTATGAAAATGACTCCCAGCAATTCTGAAACATGTGTCTTGTACAAGGAATGATTAATTGTCTAAATTTTATAATTTTATTGGGGAAAATGATTTACAATATATAAAATTAAGCATCATGAATAGTCTTAGCTCTTTAGTTCTGAAAGGCAAGGTATATGACATACTGAGATCCATTTATAAATAATTCAGGTATCAATTTAATTTGTCATGAATCAAGTGGTAAAGATACTTTCATTATTTTCTATTCTACCATAAAGAGTCTATTTAACGCAATACATTAAACTGATAAACTAAACATGTCATGGACTCTAGGTTGGTTTATAGATAAGTTTATAGAAGAGTTTATTGTACTTAAATAGAGGAGCCGAATCAACTCACAAGTATATATCCCTCCAAAAAGCCCCACACACACCTCCTAGTGTGTTATGTAATTTAGTTGGAGGCCAGCCTGATCTAAACAACAAGTTTCAGGCCAGCCAAGGATACATAGTAAGACCCGTCTCAGAAGGAAAAGGAGTTACCACTGACATAAAAAGGAACAGTCATCATATCAATGAGGAGGATCTTGAGTCAACCCCTTCCCCTCTTTAAGAAGTCTTGCTAGTGAAGCAGTGAGTGTATTGGAGTCACATACAAGAACATTTGGAAATATGGCTGCATTCCTGAAAAGCCCAACTCAGCTTGGATGACACTCCTGAAAGTTTTATCCTTGGAGCTTTAGCAAGGCTTACAGACAGCTAAGCTAGTCAGAGTCTCTTCTAGAGGGCTTGTTCACTGTTTCCCATAACGTTGTGGAGGGGCCTACTGAAAGCTGTTGGTCTCAAAATCATCCTGAGATTTGTGGGGTTTTTACTTCTTGAATCTCATGAGCTACTAAGACAGAATGTTCCAGTTTGGAGAAAATCACTATGTGGCACCCTCCCTTTTTTCTGACATGCCTCTGAGGAAAATTGGTAAAGTTAGATAATTGCACCACTAAATGTAGATCAGCTCCATGAAAATGTTGAGATATATATATATATATATATATATGTATATAAAATCAGAGAGTTTTCCTCAATATGTGTATATATGTGTATATAATTCCACCATTAAATGTATTAAATGTATTAGGATCCATGAAAATGCCTATATATGTGCACACACACTATATATATATATATATATATATATATATATATATATATAATCTTTCCTCAATATATGTACTATAAACAATTCCACCATTAAATTTAATAGGATCAATGAAATGTATGCACATATTGCATATACATATAATCATACAGCTATTCTCAGCAAGTAAGAGGACTGCAGTATGTCAGCTTCTATACATTCACACATCTTGGTATCAAGAACATAGCTATTCCAAACCAATATAGGTTCTACATATTTGTAGGTAACTGTGGGATGTTAGATATATTTTATATCTTACAACAGAATTATAAACTTGCTTTATAATTCCCTGTTTGTCTTGACTAGTTTCAACACATGGAGCAGAATATTGTAGGTTAGGGACTGTATACTCCATATATACATTCATAACTGTGCAGGTAGAATGAGTCTGAGCAAGCATTTTGTTGACTTTATATGTATTTATACAAATGTCTTACCTATCTCAGATGAAGGGAGCATAGCATTCATGTTAAAGATGGTAAATGAGAAGATATTGTTGTTTCATTATTTTAACAAGAACAGAAGAAATGATGTCACACGAGTGGCTGGAGTTTTGGGTAAGTGTCACACATAGAACTTGTAATGTGAGAGTGTGATTCAAGGATATGAATGTATGCATATCTCTGTACCCAAAGATCACAATGTGTTTGTGTATCTGATTCTGTATGTCAGGTTGATAAATCACTGAAGCTGTCATAGTTAGCTTTGAAGATCAACTTGGAACAACCCAGAATGCCCTGGGAAGGGTCTCAGTAGGGAGATTAAGCAACAGAAATATTTTATTAGTGTGCTGGGTACTAATGTTGTGACATATTCCCTATACACCGTGAAACGCAGCAAAAGGCAAACAACTGAATAAGGAGGAGATGACGGAGTTCATGAACTTAGTGGAAGAAATGGGCATTGAGGAAGAGAATGTACAGCGTATCATGGACACGGGTATAGTAGCAACCTACGTGTGTAACTTCTTACTTTGTATTTTTATAATAAATGTTATTTTTTTATTATTGAGGGTGTTGGGAAGTTGGCTCAGTGGGAAAAGTGCACACAAGCATGAGGGCCCAAGTTTGGATCCCAGCACCCATTTAGAAAGCCAAGAATAACAGAGCTGGAAAGGGGAGGGGACAAGAGGAGCTCTCTAGTAATAAATCTATCTGAAAGGTCATATTTCAAAACTAACAATGTGTAGAATGATTAAAGGAGGTGTTAAAAAGTCAGCCTCTTACCTATGCATGCGTGGGCATACACATGTCATTCACACGACTATGAACACACCAATAAACCATGCAGATAGAAACACACACACACAAAATCTACCTGAAATGAAACTCAGTTCCTAGGTCCCTCTGTCCAGATACTCTAGTCAAAACCTAGCTTTATATCTGCATTTTTATGAAAACTGTTCATATGTACTAATGTTATTACTAATATTATGTTGAAGTACTTTATTACTTTAAAATAATACTGTTGTTTTAAAATAATACTTTACTTTAAATGTTAGTATGTTAAAAATAATATATTTCCGTGTTTACTCTCCTTTAGACAACTGTCCAAGCAAGATCAAACCTTAGTGACTCAACAAGATCAGGATTAGGTGAGTCAAAGCACATTAATTTTATATCTTGAAGTTTTAATTTTAATTTTATTTTAATATTTAAGTTATTAATATTTAATATTTAAAGTAAATAATATTTTATTTGTTCTTTATCCTTTTCATATATTTATATAATGTATATTTATCTTTCATACTTCCACACACCTCATCCAAGCAACACATCTCCCTCTATACTTCATGGCTTTTAAATTTTATTATTATTTATTATTATTATTACCTCAATGAATCCAATTGGTGCTATTTCTGAATAGGGTATGTCAATTCCTGGAGGCATGAGTAATGTAATATACCAGGGCTATTATGTAATATAAAAAAATGGACTGCAGGGAGCTGGTGGCACATGCATTTAACCTAGCGCTCAAGAGGCAGAAGCAAGCATATGTCTGCGTTTTAGATAACCCTAGTCTACAGAGTGAGTTCCAGGACAGCAAGGGCTACTCAGAGAAACCCTGTCTCATAAAACCAAAAAGTATATTTTTTAAAGGCAGAAGAGGAAAGGAGGGAGGGAGGGAGGGAAAGAGGCAGACAGACAGACAGGCAGGCAGGCAGGCAAAAAGAAGGAAAAAGAAAAATATGGACCCTCCCTCTCCCAGAAACTATCAACTGGCAATAGCTCTTTGGTGGGGGGGGGGGGTCCTGAATCCCTCTCTGCTCAATTCTAGAATGTTAATTAGCTTGATCTGACCAGGGTCTTGTGCAGAACACCACAGTTGCTGTGAGTTCATGATTGTAACAGATCTGTCATGTTCAGAAAACAGAATTTTATGGCTCTACTCCCCATCCAGATGATAATTGATGGCTAAGCATCCACAGTCACTTGTCCTCATCCTTTGACCAGCTACAAATTTCTGCACAAACCACTCCCCACTGTAAAAAGTTGAGCAGAAGTCAAACATGGAGGCACACACCCTTAATCCCAACACTTGGGAGGCACGGGTAGATGAATCTCTGTGAGTATCAAGCCAGCCTGATCTACATACTGAGCTCCAGAAGATCCAGGTACATAGTCTCTATCTAAACAAACAAACACAAAGTTAAAAAGTTGATTTGACCAAAATTGAGAGAAGCATAAATCTATGAGTATTTTTAAGACCGTGGCTTGGAAACATGACAGTTCATCACCACTGGTCTCCTTCATAGGCTCCATGAGCTCCATTGTCACAGGCTTTTGACTCGAATTACAATAGAAACCCACCCTTACCCCTGTTCTTCCATAGATATGAAGTTCCTTCCATGGAGCTGGCATGAAATTTAATCAGAGAGTGCTTGGCTCCCCAATACAGCCTTTATTGCACCAGTGGACGCAAGGATGATTTTATAGTGTGTTGGGGAAGCATGGTGACATCACTGACATCTTATCCCACATACACAGCCTATTAAGTACATCTAAGCACTGTGAACGAGTTTCCTAGTCCATTTGACATCGATTTCTTGATGCCCTACAGCCACAGCATTTGGTGTCTTCAGCAATAGTGCCCTACCATTTAGATATGGTGTATAGTCAAGAGATATGGCAATAGCCAAGTTATTTTGGTTATTCCAAGGCTTCCTTCCATTAATAAATATCATGGTGGTACCCCCATGACTAAAAATTAGATTTTCACTGAATAAACCATGTCTTCTGGGAACAGCATTATACCATTGCAGGGATCCTCTGCTGAAACTTTTTTAATACTATATTTTTACTTAGCTTACAAACTAGTGGATTTCTGTAAGACTTCATTTACCTTCAGTTTCAGTTGACCCTCCCCTACCCTGTTCTTCCCTATGCCCAAACACATCCACACCTACTCCTCTAGCCCACAGCTCTCACTTTCTAATCTTCCCTGTCACCAGTGCCCAATTATATCGCCTGTATTATTATATTTTAATCACACAACCATAGGTTTCCATATGAGGTTTTAATAACCCTTCATTCTGGTTAAACCTTCCACCACACCCTGATTTCCCCATTCCACAACCAACTCCATGATTAAGCCTTCCTGCCCCAAGTATTCTTCTTTATACTTCATTTTAATGGCATTACATTTGATGGACCCACTTCCTTGATGGACCCAATTCAAACCAGTTTCTAATTACCTGGATTCCTTACATACTCCATATTATGCATACAAAATAAAAGATTCAAGTCTAATGTCCACATGTGAGATAGAATGTGCAGTTTGTCTTTCTGAGCCTGAGTGGCCTCATTAAGTATAATAATTTCCAGTTCCTTCTATTTACTTGGAAATTTCATATTTTCATTGTTCTCTATGGCTGAGTAATATTCCATCTTATACATTACATTTTCCTTATCCATTCATTAGTTGATGAACAGTTGGGTCAACTTCGTTTCTTAGCTATTATGAACTTAACCTCAGTGAGCATGGACATTCAAAGGTCTCTGTAACAGAATATAAACCCCTTTGTGTACATATCTAGAAATGGAGGAACTAGAGAAAGCACCCAAGGAACTAAAGGGAACTGCAACCCTATAGGTGGAACAACAATATGAACTAAGCAGTACCCCGGAGCTCTTGTCTCTAGCTGCATATCTATCAAAAGATGGCCTAGTCGGCCATCACTGCAAAGAGAGGCCCATTGGACTTGCAAACTTTATATGCCCCAGTACAGGGGAATGCCAGGGCCAAAAAGGGGGGATGGGTGGGTAGGGGAGTGGGGGGGGGTTGGGGACTTTTTGTATAGCATTGGAAATGTAAATGAGCTAAATACCTAATAAAAAATGGAAAAAAAAAGAAATGGTGTAACTGAGTCACATGGGAAGTCTTTTTCTAATCTTTGGATTTGTTTATTTGATGTTCATAGTTTTTGGGTTTTGGTTGGTTTTGTTCTAAGTTCTTTGTATATTGTAGACACTAATCCTCCATCACATGTGTAGTTGGCAAAGATCTCCATTCCCCGAGATACCTGTGCATTTAATTGACAGCTTCCTTTGCCGTAGTTTTTAATTCCATGATATCTGACAAGTGTTTGTCTTACTTTCTTGCTACAAGAATCCTATTCAAAGAATCCATACCTGTGTCTATGGTTAACACACACTCCATGCTTTCTTCTCTATCAGCTTCAGGTTACCATGTCTTATGACACGGTCTTTGAATCATTTGGAGTTGAGGTTTTTTTCAAGGTGACAGGGAAGAGCCCAGGTTCATTTCTCTGTATCCTGATGTCCACTTTTTCCTATTCGGTCTATTTATGGAATTATATATTTTTATGTTAGGTCATTTTTCAGTGGAGGCATTAACAATATCCAGAAGGGGACTATTTCTTACTAGTGTTGAGATGGTATTCTCCTATATGGGGCTGGTACTGAAGGCAGCAAGTTCTACCCCTAGTCTTCCTGTGAGATTCAACTACTATCTGGGACCTCGAGTGAGACTCTGTCTGTAGGATACATGGGGCTTGGTAAACTCCAATGTGAAACAAAAAATATATAATTTTAGTTTAGATTCATAGAAACTACATCCTCAAATAAACACATAAGTTCTAAAAAGTACCAATTTAGGTCTTGATATAAGATCATTTGTCATATAAAAATTTTCCATATAAGGAAAATTTCCATACAAAGTTCATGTATATTTCCAAATATACAAAATTCTGTAAAATGTTTTTGCATGATACATCTTGTCATTGTTTGCCTCTTTAATGGCTTGTATTTGTTTCATTTTCTACTCTCATCAAATATCATGTATTACTATCCTAAATATATGAAATAATTCTGTTCCAGCATTACAGATGACATCAGGAATTTTCCAGTATATTTTTCCTGGAACCTGAAACATCAATATGAAGATGAAGCAATCTTGTCTCTCAGATCATATTTTCCTATTTATTGCAAATTACAATTCCTGTCTCTGTACTTTCTCTTTCACTCATTGTTTCCCATGTTCTAATCGGTATTAGTGCATCTTTGAATGTTTAAATAAATTTATTTTACTTGC
  RefSeq DNA ID [e.g. NM_203373]    Ensembl Gene ID
1                      NM_017471 ENSMUSG00000000003

You will get back the BioMart website attributes name instead of the biomaRt package attributes name. 

Hope this helps,

Regards,

Thomas