same xloc id but different tcons id with same exons

madsaan

Member

Join Date: Jan 2011

Posts: 26
- Share
- Tweet
#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
- Tweet
#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

Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by GATTACAT

Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
- Channel: Articles
07-01-2026, 11:43 AM
Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by SEQadmin2

I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

Here are nine questions we think about, in roughly the order they matter, before...
- Channel: Articles
06-18-2026, 07:11 AM

Topics	Statistics	Last Post
High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2 Started by SEQadmin2, Yesterday, 11:08 AM	0 responses 6 views 0 reactions	Last Post by SEQadmin2 Yesterday, 11:08 AM
New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2 Started by SEQadmin2, 06-30-2026, 05:37 AM	0 responses 11 views 0 reactions	Last Post by SEQadmin2 06-30-2026, 05:37 AM
Large-Scale Protein Screen Uncovers Hidden Regulators of Alternative Polyadenylation by SEQadmin2 Started by SEQadmin2, 06-26-2026, 11:10 AM	0 responses 19 views 0 reactions	Last Post by SEQadmin2 06-26-2026, 11:10 AM
Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2 Started by SEQadmin2, 06-17-2026, 06:09 AM	0 responses 53 views 0 reactions	Last Post by SEQadmin2 06-17-2026, 06:09 AM

Unconfigured Ad

same xloc id but different tcons id with same exons

Comment

Latest Articles

ad_right_rmr

News