[ensembl-dev] Pseudogenes

[Denise Carvalho-Silva]

Dear Duarte,

This is what I've found: we've got ENSG00000225933 which matches the location of RPS14P5 but has not been cross referenced to it

http://www.ensembl.org/Homo_sapiens/Share/8c89bfc3622b6285805b2cc126330452177451441

http://www.ensembl.org/Homo_sapiens/Gene/Matches?db=core;g=ENSG00000225933;r=2:87653716-87656517;t=ENST00000452984

(note 1: RBS14P5 is available in Ensembl as RefSeq gene models from using the NCBI GFF3 files)
(note 2:  the orientation of our locus which was manually annotated by HAVANA is different from what Entrez Gene reports on http://www.ncbi.nlm.nih.gov/gene/7845)

Regarding the microRNA, we can find its GFF3 import in Ensembl

http://www.ensembl.org/Homo_sapiens/Share/f817ffc667f2e65e2e9e76905dac5b39177451441

which overlaps our current ENSG00000266070 and has been cross referenced to MIR3960 instead of MIR2861

http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:41595

It could be a good idea to contact HAVANA and see if they can manually annotate this ncRNA.

Cheers,
Denise

On 10 Feb 2015, at 10:43, Duarte Molha wrote:

> Dear Team
> 
> I have this pseudogene: PAFAH1B1P1 HGNC:8577
> and 1 microRNA: MIR2861  HGNC:38221 
> 
> Is there a way to retrieve this pseudogene and microRNA genomic locations on ensembl database using the API and is HGNC symbol?
> 
> I have used:
> 
>  my @fetched_genes = @{ $gene_adaptor->fetch_all_by_external_name($query_gene) };
> unless (@fetched_genes){
> 	@fetched_genes = @{$gene_adaptor->fetch_all_by_display_label($query_gene)};
> }
> 
> and it fails to query these 2 features using API v78. Its there another approach I should be using?
> 
> 
> Refseq entries for both:
> 
> http://www.ncbi.nlm.nih.gov/nuccore/NG_003165
> http://www.ncbi.nlm.nih.gov/nuccore/NR_036055
> 
> Best regards
> 
> Duarte
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