RefSeq Version for Hg19 data

[Genetics Savvy]

Hi, 

I had downloaded the RefSeq genes data from the UCSC table browser for genome version Hg19. 

When i looked into the "describe table schema" it said it was last updated on  2016-08-16 but it didn't talk about the version of RefSeq used.

If you could confirm the version of  RefSeq data ? 

Steps taken to download the data - 

Clade       - Mammal

Genome   - Human

Assembly - Feb.2009 (GRCh37/hg19)

Group       - Genes and Gene Predictions

Track       - RefSeq Genes

Table       - refGene

Much Thanks,

Savvy 

[Cath Tyner]

Thank you for using the UCSC Genome Browser and for inquiring about the versioning information for refGene. You can access the version number by adding a related table to your query.

Start at the Table Browser with the following fields set:

Clade - Mammal

Genome - Human

Assembly - Feb.2009 (GRCh37/hg19)

Group - Genes and Gene Predictions

Track - RefSeq Genes

Table - refGene

For this example, I'll paste in an identifier, "NM_000454"

For "output file" select the option "selected fields from primary and related tables" and click "get output" to go to the next step.

Under the "Select Fields from hg19.refGene" section, I'll select the "name" and "name2" checkboxes.

Under "Linked Tables," select the checkbox for "hgFixed: gbCdnaInfo"

Now, select the button, "allow selection from checked tables."

Under "hgFixed.gbCdnaInfo fields" you can select "version" and then click "get output."

Example output:

#hg19.refGene.name hg19.refGene.name2 hgFixed.gbCdnaInfo.version

NM_000454 SOD1 4

You can compare this to the NCBI reference at http://www.ncbi.nlm.nih.gov/nuccore/48762945

ACCESSION   NM_000454

VERSION     NM_000454.4 

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Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Cath Tyner]

Hi again Savvy,

I misunderstood your question, my apologies. The RefSeq release version can be found through a MySQL query on the hgFixed database using the gbLoaded table.

Information about connecting to the MySQL public database: https://genome.ucsc.edu/goldenpath/help/mysql.html

mysql> select loadRelease from hgFixed.gbLoaded where srcDb="RefSeq" and time -> < "2016-08-16" order by time limit 1;

+-------------+

| loadRelease |

+-------------+

| 77          |

+-------------+

More information from NCBI: http://www.ncbi.nlm.nih.gov/news/07-07-2016-refseq-release77/

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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