[ensembl-dev] ribosomal rna annotations in human grch37

Hardip Patel H.Patel at victorchang.edu.au
Tue Dec 21 07:38:42 GMT 2010


Hi All

I was just wondering about Ribosomal RNA 28S and 18S annotations in Ensembl v60 (v59 as well) for human genome.

For 28S rRNA, ensembl gene ID is ENSG00000226958. My concern is why this gene is labeled as processed pseudogene and not a rRNA gene?
Second concern is that NCBI refseq (ID NR_003287) corresponding to 28S rRNA is 5070 bp long but the transcript of the gene annotated as 28s rRNA in ensembl ( ENSG00000226958) has a length of some 432 bp.

However, searching for NR_003287 in the ensembl, it returns  GL000220.1  as the perfect match over the entire length with lots of miRNA annotated in the contig, a 5.8S subunit annotated but not the 28S rRNA.

Can somebody please explain me this discrepancy?

Any help is greatly appreciated.

Thanking you

Regards

--
Hardip R. Patel
Bioinformatician, Molecular Genetics Division,
Victor Chang Cardiac Research Institute,
Darlinghurst, NSW - 2010, Australia
(W): +61 - 2 - 9295 8611
(M): 0449 180 715

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