Why Is The Rag Gene Missing In The Ucsc Xenopus Genome?

Question

[anuragm]

I couldnt find any gene corresponding to RAG on the ucsc database.

Is RAG available in the browser under some other name ? I googled for synonyms of RAG and came up with RNF74, MGC43321, LOC5896, but I dont get hits for any of these in the Xenopus genome.

Am I doing anything wrong ?

Answer 1

[Alastair Kerr]

I'm not sure about UCSC, but I advise on never using common names when searching for a gene as these can be confusing and often differ across different model organisms. Indeed RAG is not even a standard gene name in human: HGNC use KPNA2 for karyopherin alpha 2 (RAG cohort 1, importin alpha 1).

Better ways to search are using the sequence (BLAST) or looking at pre-calculated orthologs e.g. http://www.ensembl.org has this calculated for most common organisms. In this case kpna2 = ENSXETG00000001594 in Xenopus

Moreover if the terms ortholog or paralog confuse you, I highly recommend that you take some time learning the definitions and how these are calculated. The wikipedia page on homologs are a good place to start, as is the Ensembl help page on how they do their calculations