Transcript NM#s for different types of transcripts

Question

[reneebend]

Dear Professors,

I am working on a project where I need to find both the longest transcript (and NM#) and the HGMD transcript (and NM#) for a list of over 100 genes. Then I need to see if these two match.

I have figured out a way I can do this clicking through many links on the UCSC genome browser page, but I'm wondering if there's an easier or quicker way to access this information.

Thank you!

NCBI-NOW! Student,

Renee Bend

[Ram]

You can use UCSC's MySQL access to get this information. You can fetch all mRNA sequence IDs (NM_*) for a gene and query the gbSeq table with them to get their size (or use HAVING to pick the one with the max size).

[reneebend]

Hi, Thank you so much for your answer, but it seems like I may need an alternate route, at least for the time being, as I am not yet able to download MySQL.

Do you have any ideas for being able to do this fully online?

Thank you,

Renee

[reneebend]

I have come up with a way to get some of the information I need, though I still haven't figured out how to get an amino acid count.

I am using BioMart.

Dataset: Ensemble Genes 82, Homo sapiens genes (GRCh38.p3)
Filters: GENE: Check box - Limit to genes (external references) with RefSeq mRNA IDs;

            Input external references ID list [Max 500 advised], and input list of genes as HGNC symbols [e.g.NTN3]

Attributes: Features:  GENE: Transcript Length (including UTRs and CDS), APPRIS Notation

                            EXTERNAL: RefSeq mRNA [e.g.NM_00195597], HGNC Symbol, RefSeq Protein ID [e.g. NP_001720922]

RESULTS, Export to excel file.

Again, at this point I am clicking on individual XP_IDs to get the amino acid length for each protein, and note which one is the longest. Any tips for automating this part would be helpful. I still don't have authorization to download MySQL.

Thank you!
Renee

[Ram]

See if Galaxy can help you run queries to UCSC MySQL