2 transcript_id values for the same tRNA in GTF file

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3.7 years ago

hashkolnikov • 0

Hello, everybody. I'm testing a script i made to filter some information from a GTF file and while looking through the file i saw this:

ChrM Araport11 uORF 143781 144104 . + . transcript_id "ATMG00030"; gene_id "ATMG00030";

ChrM Araport11 gene 149673 149743 . + . transcript_id "trnfM(CAT)"; gene_id "ATMG00030";

ChrM Araport11 tRNA 149673 149743 . + . transcript_id "ATMG00030.1/ATMG00280.1"; gene_id "ATMG00030";

ChrM Araport11 exon 149673 149743 . + . transcript_id "ATMG00030.1/ATMG00280.1"; gene_id "ATMG00030";

ChrM Araport11 uORF 164947 165278 . + . transcript_id "ATMG00280"; gene_id "ATMG00280";

I would like to know what does it mean for the tRNA and exon lines to have 2 transcript_id values. I downloaded the GTF file from this page: https://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FGenes%2FAraport11_genome_release

GTF arabidopsisthaliana annotation • 859 views

ADD COMMENT • link updated 3.7 years ago by Santosh Anand 5.8k • written 3.7 years ago by hashkolnikov • 0

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Seems to be an anomaly or annotation mistake/update (with reference to old id), also because it occurs (2 trans id) only once in the whole GTF file

ADD REPLY • link 3.7 years ago by Santosh Anand 5.8k

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