Question: [Hg19.Gtf] Why Is The Same Transcript Annotated As Multiple Isoforms??
1
gravatar for Leszek
7.4 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

Why is the same transcript (chr1:1572770:1572875) annotated as multiple isoforms (CDK11B,CDK11Bdup1,CDK11Bdup2,CDK11Bdup3,CDK11Bdup4,CDK11B_dup5) in hg19?

chr1    hg19_refFlat    CDS    1572770    1572875    0.000000    -    0    gene_id "CDK11B"; transcript_id "CDK11B"; 
chr1    hg19_refFlat    exon    1572770    1572875    0.000000    -    .    gene_id "CDK11B"; transcript_id "CDK11B"; 
chr1    hg19_refFlat    CDS    1572770    1572875    0.000000    -    0    gene_id "CDK11B"; transcript_id "CDK11B_dup1"; 
chr1    hg19_refFlat    exon    1572770    1572875    0.000000    -    .    gene_id "CDK11B"; transcript_id "CDK11B_dup1"; 
chr1    hg19_refFlat    CDS    1572770    1572875    0.000000    -    0    gene_id "CDK11B"; transcript_id "CDK11B_dup2";     
chr1    hg19_refFlat    exon    1572770    1572875    0.000000    -    .    gene_id "CDK11B"; transcript_id "CDK11B_dup2"; 
chr1    hg19_refFlat    CDS    1572770    1572875    0.000000    -    0    gene_id "CDK11B"; transcript_id "CDK11B_dup3"; 
chr1    hg19_refFlat    exon    1572770    1572875    0.000000    -    .    gene_id "CDK11B"; transcript_id "CDK11B_dup3";     
chr1    hg19_refFlat    CDS    1572770    1572875    0.000000    -    0    gene_id "CDK11B"; transcript_id "CDK11B_dup4"; 
chr1    hg19_refFlat    exon    1572770    1572875    0.000000    -    .    gene_id "CDK11B"; transcript_id "CDK11B_dup4"; 
chr1    hg19_refFlat    CDS    1572770    1572875    0.000000    -    0    gene_id "CDK11B"; transcript_id "CDK11B_dup5";
chr1    hg19_refFlat    exon    1572770    1572875    0.000000    -    .    gene_id "CDK11B"; transcript_id "CDK11B_dup5"; 
ADD COMMENTlink written 7.4 years ago by Leszek4.0k
4
gravatar for Neilfws
7.4 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

The region chr1:1572770 - 1572875 is not the same transcript; it's the same exon. 105 bp would be rather small for a transcript.

So there are multiple alternative transcripts for the gene CDK11B - at least 6 according to Refseq and 5 according to Ensembl - and all of them contain that exon.

Try starting from this view in the genome browser and zooming out, until you start to see the structure of the transcripts.

ADD COMMENTlink written 7.4 years ago by Neilfws48k
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