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

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";

hg annotation transcript isoform gene

• 4,295 views • link

updated 14.6 years ago by Neilfws

• written 14.6 years ago by Leszek

1 answer

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.

• 0 views • link

written 14.6 years ago by Neilfws

More posts like this

RNA-Seq error in htseq-count
written 8.1 years ago by elb

Hi guys, I really do not know what is happening to my RNA seq data analysis pipeline and hence I'm looking for some help. Although …
Problem with loacting gtf file
written 8.7 years ago by elisheva

Hi everyone! I have this expression file (UCSC genes, hg19): tracking_id FPKM FPKM 0 FPKM_status FPKM_status DDX11L1 0.0220335 0.014392 0.0182127 OK OK WASH7P 0.325992 0.242878 …
Does CDS, start_codon and stop_codon in gtf affect transcriptome assembly by StringTie?
written 10.2 years ago by syrttgump •

Hi All. I am using StringTie to assemble transcriptome from my RNA-Seq data. The question is that if I use refSeq as reference annotation which …
Inconsistent GTF from UCSC browser vs genePredToGtf
written 10.2 years ago by dariober

There seem to be some inconsistencies between GTF records from [UCSC table browser][1] and from files generated with `genePredToGtf` (from [UCSC utilities][2]). For example, on …
Quantification of RNA-Seq bam files (STAR + HTSeq count)
written 10.6 years ago by ChIP

Hi All, I am working with pig genome and I had received some FASTQ transcriptome files from my lab mates. I have processed the FASTQ …
Mapping a de novo built transcriptome to a reference transcriptome
written 11.4 years ago by cyril-cros

Hi, I am interested in building an updated annotation of the mouse olfactory receptor genes. They have a tissue specific expression obviously, with various 3' …
How To Handle 'Mate Mapped To Different Chr' In Rna-Seq Data Analysis ?
written 12.6 years ago by GouthamAtla

I have aligned my paired-end reads to Hg19 build from Ensemble using tophat2. Tophat 'align_stats.txt' shows that 96% overall alignment. The command I used is …
Ensembl And Ucsc Gtfs To Match
written 12.8 years ago by dfernan

Hi, I'd like to transform a ucsc gtf file that I downloaded from the table browser to an ensembl-gtf-like format. I.e., I'd like …
Htseq-Count Error With Strand-Specific Data
written 13.4 years ago by Nicolas Rosewick

Hi, I have 2x50 bp human strand-specific data. I aligned them against hg19 with STAR and after that I extracted the read count per gene …
What Does Cds And Exon Mean In A Gtf File?
written 13.4 years ago by dfernan

Hi, I have a hg19 GTF file that I ordered according to chromosome start and end positions, and group by gene_id. Here is an …