same xloc id but different tcons id with same exons

madsaan

Member

Join Date: Jan 2011

Posts: 26
Share

Post
#1

same xloc id but different tcons id with same exons

05-16-2011, 07:33 AM

Hello,

I am trying to find differentially expressed genes bteween two samples and looked at the cuffcompare.combined.gtf file and noticed the following

chr9 Cufflinks exon 18970198 18970476 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "1"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19048355 19048421 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "2"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19058189 19058237 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "3"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19058815 19058928 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "4"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19060579 19060698 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "5"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19061925 19062041 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "6"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19062708 19062759 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "7"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19064835 19064962 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "8"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19066041 19066118 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "9"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19067507 19067646 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "10"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19075231 19075250 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00002983"; exon_number "11"; gene_name "ENSCAFG00000010758"; oId "gonad.26568.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1239";
chr9 Cufflinks exon 19048370 19048421 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "1"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";
chr9 Cufflinks exon 19058189 19058237 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "2"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";
chr9 Cufflinks exon 19058815 19058928 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "3"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";
chr9 Cufflinks exon 19060579 19060698 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "4"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";
chr9 Cufflinks exon 19061925 19062041 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "5"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";
chr9 Cufflinks exon 19062708 19062759 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "6"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";
chr9 Cufflinks exon 19064835 19064962 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "7"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";
chr9 Cufflinks exon 19066041 19066118 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "8"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";
chr9 Cufflinks exon 19067507 19067646 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "9"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";
chr9 Cufflinks exon 19075231 19075276 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "10"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";
chr9 Cufflinks exon 19081324 19081659 . + . gene_id "XLOC_001684"; transcript_id "TCONS_00004682"; exon_number "11"; gene_name "ENSCAFG00000010758"; oId "gonad.30133.1"; nearest_ref "ENSCAFT00000017124"; class_code "c"; tss_id "TSS1240";

Why am I getting different TCONS ids when the exon numbers are the same?

Thanks,
Joji
Tags: None
hchang10

Member

Join Date: May 2013

Posts: 13
Share

Post
#2

10-09-2014, 05:46 AM

I noticed this too. If anyone could explain the differences between XLOC (gene id) and TCONS (transcript id), I'll really appreciate.
Comment

Previous template Next

Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t

by SEQadmin2

Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...
- Channel: Articles
10-14-2026, 09:55 AM
New Genomics Technologies Take Aim at Long-Standing Limits

by SEQadmin2

Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
- Channel: Articles
09-28-2026, 10:25 AM

Topics	Statistics	Last Post
Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2 Started by SEQadmin2, 10-15-2026, 10:52 AM	0 responses 30 views 0 reactions	Last Post by SEQadmin2 10-15-2026, 10:52 AM
Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2 Started by SEQadmin2, 10-14-2026, 05:39 AM	0 responses 37 views 0 reactions	Last Post by SEQadmin2 10-14-2026, 05:39 AM
Larger Datasets Reveal Additional Switches That Control Gene Expression by SEQadmin2 Started by SEQadmin2, 10-13-2026, 09:56 AM	0 responses 31 views 0 reactions	Last Post by SEQadmin2 10-13-2026, 09:56 AM
Computational Tool Captures How Chromatin Folds at Scale by SEQadmin2 Started by SEQadmin2, 10-09-2026, 11:14 AM	0 responses 29 views 0 reactions	Last Post by SEQadmin2 10-09-2026, 11:14 AM

Unconfigured Ad

same xloc id but different tcons id with same exons

Comment

Latest Articles

ad_right_rmr

News