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What Are These Rp11 'Genes' In The Genome?
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6.5 years ago
Rubal7 • 760

Hello Everyone,

I am looking at genes within certain genomic windows in the human genome and keep coming across clusters of genes starting with RP eg RP11-142L4.2 RP11-592B15.4 RP3-419C19.2

They seem to be really abundant but I can't find what the RP stands for anywhere. Are these real genes, their adundance makes me suspect they are something like pseudogenes or transcripts of unknown function.

Any help on this really appreciated.

Best,

Rubal

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many of the RP11- are actually linc-RNAs

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Hi, You may even look into this page : http://www.sanger.ac.uk/research/projects/vertebrategenome/havana/

Which is the havana project page from the Sanger sequencing offshoot. These genes are manually curated from that project. There is a bit of confusion about whether these are pseudogenes are not but the annoation fro pseudogenes is a bit different it will be "rpL" and not just "RP"

best

-M

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Are these the Pseudogenes!!

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Ribosomal protein pseudogenes? Thanks for clearing that up

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6.5 years ago

RP11 is a code identifying an individual anonymous human donor to a The BAC clone library started at Roswell Park Cancer Institute by Dr.Pieter de Jong. Initially, samples were obtained from 10 men and 10 women. During the processing of the samples, DNA from one individual (RP11) emerged as the best quality most complete set and became the source for much of the BAC clone library that much of the Human Gnome project studied. As new genes were discovered and named, the names include the source info "RP11."

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Mark - do you have a reference for this?

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4.9 years ago
jeales • 110
United Kingdom

I reckon the "RP11-" gene names come from IDs for BAC clones which contain the gene. The clone ID (e.g. "RP11-1000B6") is affixed with incrementing integers to denote the different unnamed genes found on it e.g. "RP11-1000B6.2" and "RP11-1000B6.3" (these are real by the way) Some get renamed to something descriptive of the gene or gene products, but those that remain uncharacterised keep the RP11- name

see here for the RP11 clones http://genome.ym.edu.tw/libres/RP11%20bac%20Information.htm

However genes with "RPL" names do indeed seem to relate to ribosomal protein pseudogenes

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Just to be clear, only gene names beginning with "RPL" are ribosomal protein psedogenes. "RP11" genes are essentially unnamed genes, that are given a unique name based on their containing human genomic BAC library clone name

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I retract my answer

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Indeed the "RP11-" gene symbols come from the manually annotated Vertebrate Genome Annotation (Vega) database, as explained in Ashurst _et al._ , 2005: " _If an approved symbol is not available for a gene locus, an interim internal identifier is used, which is usually in the format clonename.number, e.g. RP11-694B14.5_ ".

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