Hi, I downloaded the hg18 refGene gff from UCSC table, and noticed that if a refGene transcript was mapped to more than one locations, '_dup' was added to the refGene ID. For example: NM_001005277_dup1. In the case of NM_001005277, it mapped to 3 locations in genome, two of them mapped to chr1 and one mapped to chr5. I thought it would be NM_001005277, NM_001005277_dup1, NM_001005277_dup2. But actually, the gff file had NM_001005277, NM_001005277_dup1, NM_001005277. Both chr1 and chr5 has the same NM_001005277. Is this an error? If not, could you explain the rational behind this?
chr1 hg18_refGene start_codon 357522 357524 0.000000 + . gene_id "NM_001005277"; transcript_id "NM_001005277"; chr1 hg18_refGene CDS 357522 358457 0.000000 + 0 gene_id "NM_001005277"; transcript_id "NM_001005277"; chr1 hg18_refGene stop_codon 358458 358460 0.000000 + . gene_id "NM_001005277"; transcript_id "NM_001005277"; chr1 hg18_refGene exon 357522 358460 0.000000 + . gene_id "NM_001005277"; transcript_id "NM_001005277"; chr1 hg18_refGene stop_codon 610959 610961 0.000000 - . gene_id "NM_001005277"; transcript_id "NM_001005277_dup1"; chr1 hg18_refGene CDS 610962 611897 0.000000 - 0 gene_id "NM_001005277"; transcript_id "NM_001005277_dup1"; chr1 hg18_refGene start_codon 611895 611897 0.000000 - . gene_id "NM_001005277"; transcript_id "NM_001005277_dup1"; chr1 hg18_refGene exon 610959 611897 0.000000 - . gene_id "NM_001005277"; transcript_id "NM_001005277_dup1"; chr5 hg18_refGene start_codon 180726894 180726896 0.000000 + . gene_id "NM_001005277"; transcript_id "NM_001005277"; chr5 hg18_refGene CDS 180726894 180727829 0.000000 + 0 gene_id "NM_001005277"; transcript_id "NM_001005277"; chr5 hg18_refGene stop_codon 180727830 180727832 0.000000 + . gene_id "NM_001005277"; transcript_id "NM_001005277"; chr5 hg18_refGene exon 180726894 180727832 0.000000 + . gene_id "NM_001005277"; transcript_id "NM_001005277"; Thanks, Bingbing _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
