How to change genes name

Question

[hosin]

Hi I have many many genes from Oar-V3.1.gtf ,with these names : LOC105603009, LOC105616604, LOC105605738,LOC105604038 How I can change them to real name ? Please help me.Thanks

[finswimmer]

Hello hosein_salehi6 ,

what species we are talking about? Where did you get this gtf file? I couldn't found anything about these loci.

fin swimmer

[hosin]

Actually , these loci and Oar-V3.1.gtf file are from sheep.

[Mark]

Ive seen this before, this type of naming convention is used when the predict gene has no homology to anything known/found so essentially a place holder name is given. LOC = Location.

I would blast and annotate with "predict X" but keep that locus tag.

Answer 1

[urjaswita]

This happens when either the gene is not well annotated, or if the automatic annotation pipeline (e.g. NCBI genomes) cannot determine the exact identity of the gene. You can run a BLAST search using the sequence of the gene/protein and identify which gene is this.

If this is from NCBI genomes, you can also check the description. Often they write more about the gene in descriptions for these locus numbers.

Urja