[genome] source gene names of retroposed genes

[Enrique Medina-Acosta]

Dear UCSC Genome Browser support team,

 

I wish to bulk-extract the names of the source (parent) genes for the entire set of retroposed genes, including pseudogenes, available in either hg19 or hg38.

 

For example, from the retroposed track at the Genome Browser, I see that ARL5A is the source gene name for the retro NM_012097.3-2 by clicking on the retrogene to open the information table “Retroposed Genes V9, Including Pseudogenes (NM_012097.3-2)” (see print screen attached)

 

So, I could not find the right Table that contains the information about the source (parent) gene name using either Table Browser or Data Integrator

 

Here is the path a took in Table Browser.

 

Clade: Mammal

Genome: human

Assembly: hg19 or hg38

Group: Genes and Gene Predictions

Track: retroposed genes

Tables: ucscRetroAli5, ucscRetroCds5, ucscRetroExpressed5, ucscretroInfo5, ucscretroOrtho5, ucscretroSeq5

Output format: selected fields from primary and related tables.

 

Best regards,

 

Enrique

 

 

 

 

 

Prof. Dr. Enrique Medina-Acosta, M.Sc., PhD.
MyCVLattes - CNPq
MyResearcherID (ISI Web of Knowledge)
MyORCID

Senior Associate Professor
Unit Coordinator - Molecular Identification and Diagnostics Unit - NUDIM
Laboratory of Biotechnology, Center for Biosciences and Biotechnology
Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF
Building P4, rooms 212/228
Avenida Alberto Lamego 2000, Parque Califórnia, CEP 28013-602, Campos dos Goytacazes, RJ, Brazil.
Tel: +55 22 27397085

[Christopher Lee]

Hi Enrique,

Thank you for your question about bulk extracting source gene names for the Retro Genes track. Unfortunately, the query used to extract this information is unsupported in the Table Browser, and so in order to bulk extract these data, you will need to query our public MySQL server, which requires access to a command line and having MySQL installed on your machine. Once you have this set up, the following command will extract the source gene information for the hg38 RetroGenes 9 track:

mysql --host=genome-mysql.soe.ucsc.edu --user=genome -A -Ne "select r.name as id, gene.name from hg38.ucscRetroInfo9 r, hgFixed.geneName gene, hgFixed.gbCdnaInfo g, hgFixed.description d where (substring(r.name,1,locate('.', r.name)-1))=g.acc and g.geneName=gene.id and g.description=d.id" 

This query results in output like the following:

A22930.1-6    n/a
A22938.1-11    n/a
A22938.1-14    n/a
A22938.1-21    n/a
AB002312.2-5    KIAA0314
AB004304.1-75    n/a
AB004304.1-84    n/a
AB009619.1-2    n/a
AB011119.1-179    KIAA0547
AB011539.2-17    MEGF6

Where the first column is the retro gene name and the second column is the source gene name (if it exists). If you want information for the hg19 track, you will only need to change the database and table info from "hg38.ucscRetroInfo9 r" to "hg19.ucscRetroInfo5 r".

For more information about using our public MySQL server, please see the following page:
http://genome.ucsc.edu/goldenPath/help/mysql

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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