What Are These Rp11 'Genes' In The Genome?

Question

[Rubal7]

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

[Gema Sanz]

many of the RP11- are actually linc-RNAs

[man.karhade]

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 annotation for pseudogenes is a bit different it will be "rpL" and not just "RP"

best

-M

[Sukhi Singh]

Are these the Pseudogenes!!

[Rubal7]

Ribosomal protein pseudogenes? Thanks for clearing that up

Answer 1

[markjlvanderwater]

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."

[Jonathanjacobs]

Mark - do you have a reference for this?

[Kevin Blighe]

I will answer for Mark 5 years after the fact, curiously via job advert at Roswell Park: https://www.roswellpark.org/careers/clinical/clinical-and-translational-director-next-generation-sequencing

In case the link expires:

RPCI was the first institution to focus exclusively on cancer research and continues to be at the center of groundbreaking cancer research for more than a century. This includes initiating the first experiments in chemotherapy in 1904, becoming America’s First Comprehensive Cancer Center and providing the source — RP11 (RP stands for Roswell Park) — for much of the BAC clone library used in the Human Genome Project. The breakthrough research, scientific expertise, and commitment to improving patient care is the foundation of OmniSeq today. Visit http://www.omniseq.com to learn more.

Answer 2

[jeales]

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

[jeales]

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

[Ido Tamir]

I retract my answer

[Charles Plessy]

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”.