As you can see, for Exon1 the transcript ID is ENSMUST00000070663.5 and exon number is 6
But exon2's transcript id is ENSMUST00000219068.1 and exon number is 1
I have checked a few correct entries, both exon1 and exon2 referenced the same transcript id.
Hi,
I am doing circle detection in mm10. starchip v1.3e.
When I looked at the *.genes file, I have found many chimeric junctions with Exon1 > Exon2 regardless of the strand.
E.g. Exon1 is 6, Exon2 is 1
control1.circRNA.3reads.1ind.genes:chr10:108240105-108252924 Ppp1r12a 6 1 + Exon-Exon
A possible explanation might be due to the incongruent transcript_ids of the Exon1 and Exon2. E.g. In the corresponding *.annotated file
chr10:108240105-108252924 gene_id:"ENSMUSG00000019907.10";transcript_id:"ENSMUST00000070663.5";gene_type:"protein_coding";gene_name:"Ppp1r12a";transcript_type:"protein_coding";transcript_name:"Ppp1r12a-201";exon_number:6;exon_id:"ENSMUSE00000256576.1";level:2;protein_id:"ENSMUSP00000069257.5";transcript_support_level:"1";mgi_id:"MGI:1309528";tag:"basic";tag:"CCDS";ccdsid:"CCDS36052.1";havana_gene:"OTTMUSG00000064091.1";havana_transcript:"OTTMUST00000156627.1"; + 0 gene_id:"ENSMUSG00000019907.10";transcript_id:"ENSMUST00000219068.1";gene_type:"protein_coding";gene_name:"Ppp1r12a";transcript_type:"retained_intron";transcript_name:"Ppp1r12a-204";exon_number:1;exon_id:"ENSMUSE00001407709.1";level:2;transcript_support_level:"3";mgi_id:"MGI:1309528";havana_gene:"OTTMUSG00000064091.1";havana_transcript:"OTTMUST00000156630.1"; + 0
As you can see, for Exon1 the transcript ID is ENSMUST00000070663.5 and exon number is 6 But exon2's transcript id is ENSMUST00000219068.1 and exon number is 1
I have checked a few correct entries, both exon1 and exon2 referenced the same transcript id.
Is it the cause of the problem?
Thanks, Eric.