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The definition of a gene

Hi

I downloaded a gtf file for hg38; I want to annotate AC023824.3 (Ensembl transcript ID ENST00000569557.2, Ensembl gene ID ENSG00000260958.3) I got this

gene_id lnc-TP53TG3F-9 ; transcript_id lnc-TP53TG3F-9:2 ; gene_alias_1 ENSG00000260958.2 ; gene_alias_2 RP11-488I20.8 ; gene_alias_3 OTTHUMG00000176241.2 ; gene_alias_4 AC023824.4 ; gene_alias_5 AC023824.3 ; transcript_alias_1 ENST00000569557.2 ; transcript_alias_2 RP11-488I20.8-002 ; transcript_alias_3 OTTHUMT00000431667.2 ; transcript_alias_4 NONHSAT142166 ;

So, this means AC023824.3 is lnc-TP53TG3F-9 ?

Please can some one help me to know from this gtf file which part annotates AC023824.3

gene lncrna transcript
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written by zizigolu zizigolu

1 answer

AC* accessions are for contigs: https://www.ensembl.org/Multi/Search/Results?q=AC023824;site=ensembl;page=1

There are multiple genes in that contig.

genes

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written by GenoMax GenoMax

Thanks a lot

So, this means genes aliases in GTF files are located in this regions? Genes like lnc-TP53TG3F-9

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written by zizigolu zizigolu

Thanks a million

The list of genes you kindly provided supposed to be long non-coding RNAs

So, do you know how to find their target genes?

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written by zizigolu zizigolu

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