where do I find transcript_biotype

Hi newbie_r,

I am unsure; however, via biomaRt in R, one can generate a master table that has biotypes for Ensembl and RefSeq ‘transcripts’.

require(biomaRt)
ensembl <- useMart('ensembl', dataset="hsapiens_gene_ensembl")

annot <- getBM(
  attributes = c(
    'hgnc_symbol',
    'ensembl_gene_id',
    'ensembl_transcript_id',
    'entrezgene_id',
    'refseq_mrna',
    'gene_biotype'),
  mart = ensembl)

head(subset(annot, refseq_mrna != ''))
   hgnc_symbol ensembl_gene_id ensembl_transcript_id entrezgene_id  refseq_mrna
45       INTS3 ENSG00000262826       ENST00000576030         65123    NM_023015
46       INTS3 ENSG00000262826       ENST00000576030         65123 NM_001324475
62     KIR2DL3 ENSG00000273947       ENST00000616520          3804    NM_015868
66     KIR2DL4 ENSG00000276779       ENST00000618567          3805 NM_001080770
67     KIR2DL4 ENSG00000276779       ENST00000618567          3805    NM_002255
75     KIR3DL2 ENSG00000273735       ENST00000620501          3812    NM_006737
     gene_biotype
45 protein_coding
46 protein_coding
62 protein_coding
66 protein_coding
67 protein_coding
75 protein_coding

There is also the attribute refseq_ncrna that can be used.

Kevin