getting the primary transcript ID with version number

[Rajat Singhania]

Hi, is it possible to get the primary transcript ID with version number given a list of IDs such as NM_000300, i.e., without version number?  Thanks very much, Rajat

[Rajat Singhania]

Hi, I also have the gene symbols available for which I would like to get the primary transcript ID with version number.  Can anyone point to a suitable resource?  Thank you, Rajat

[Jairo Navarro Gonzalez]

Hello Bahram,

Thank you for using the UCSC Genome Browser and your inquiry.

If you have many identifiers, the best way to obtain the version number is to query our MySQL database. You can learn more about how to connect to the server from the following help page, http://genome.ucsc.edu/goldenPath/help/mysql.html. You can use the ncbiRefSeqLink table to get the name column which contains the gene symbols and the id column which contains versioned accessions. The following query will give you your results:

mysql> select id from ncbiRefSeqLink where id like 'NM_000300%';
+-------------+
| id          |
+-------------+
| NM_000300.3 |
+-------------+
1 row in set (0.12 sec)

An alternative is to use the Table Browser. You can use the following steps to get the versioned accessions:

Step 1: Configure the Table Browser

Once you have uploaded your regions as a custom track, return to the Table Browser and apply the following settings.

clade: mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: Genes and Gene Predictions
track: NCBI RefSeq
table: ncbiRefSeq
region: genome
output format: selected fields from primary and related tables

Step 2: Create a filter

Next to filter: click create.

You will be taken to a new page where you can filter for your identifier. First, select the ncbiRefSeqLink table under Linked Tables and click allow filtering using fields in checked fields. Then, change:

id    does    match    *

to

id    does    match    NM_000300*

Finally, click submit.

Step 3: Get output

Once back on the main Table Browser page, click get output. Then allow selection from the ncbiRefSeqLink table and select the ncbiRefSeqLink.id field. Finally, click get output to see the versioned accession.

I hope this is helpful. 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 Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

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