Entering edit mode
8 weeks ago
zizigolu
★
4.3k
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
Thanks a lot
So, this means genes aliases in GTF files are located in this regions? Genes like lnc-TP53TG3F-9
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
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?