ENSG-like CATG Identifier?

Question

[aaragak1]

Hello all,

I've been giving some expression data which has rather perplexing identifiers. Along with Ensembl ENSG identifiers, it also has similar CATG identifiers (eg CATG00000000004) that I can seem to find nothing about. I know the answer is probably obvious to the initiated, but I'm stumped - any help would be appreciated.

Answer 1

[GenoMax]

They appear to be from lncRNAKB. Check this site. They are also in a GTF file on same page.

lnckb.60009 chr10   100268853   100270417   FANTOM  lncRNA  gene_id_alias "CATG00000000612.1";geneSuperClass "all_lncRNA";geneClass "lncRNA_intergenic";geneSubClass "proximal_to_coding_genes_sense_strand";gene_type "__na";gene_name "CATG00000000612.1";coding_status "nonCoding";cumulative_support "ENCODE";geneCategory "__na";DHS_type "DHS_dyadic";
lnckb.66742 chr10   100286763   100287348   NONCODE,FANTOM,LNCipedia,MITranscriptome    lncRNA  gene_id_alis_alias "CATG00000116184.1";geneSuperClass "all_lncRNA";geneClass "lncRNA_divergent";geneSubClass "divergent_promoters";gene_type "__na";gene_name "CATG00000116184.1";coding_status "nonCoding";cumulative_support "ENCODE:FANTOM:HUBDMAP";geneCategory "p_lncRNA_divergent";DHS_type "DHS_promoter";

Edit: Link to the website hosting these files was refreshed in Feb 2023.

Answer 2

[Mpiro]

Hello, Yes, we have it in our lncRNAKB knowledgebase: http://psychiatry.som.jhmi.edu/lncrnakb/gene_details.php?id=lnckb.60009.chr10:100268853-100270417

The original record is actually from FANTOM: https://fantom.gsc.riken.jp/cat/v1/#/genes/CATG00000000612.1

Answer 3

[diogo.pellegrina]

The links above are 404ed, I believe this is the new one: https://osf.io/ru4d2/

[GenoMax]

Note: That link is indeed the new site that has these files. It is not a redirect. I will edit my answer above.