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Old 05-16-2011, 07:33 AM   #1
madsaan
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Location: california

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Exclamation same xloc id but different tcons id with same exons

Hello,

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

Quote:
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
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Old 10-09-2014, 05:46 AM   #2
hchang10
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I noticed this too. If anyone could explain the differences between XLOC (gene id) and TCONS (transcript id), I'll really appreciate.
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