[Hg19.Gtf] Why Is The Same Transcript Annotated As Multiple Isoforms??

Question

[Leszek]

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"; 

Answer 1

[Neilfws]

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.