The definition of a gene

Question

[zizigolu]

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

Answer 1

[GenoMax]

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.

[zizigolu]

Thanks a lot

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

[GenoMax]

These are genes located in that region: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr16%3A34146298%2D34176786&hgsid=2365629101_WnIKgnM9oAFuahMXPlApidsyck3S

[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?