Locating 3'UTR of a gene not yet annotated

[Abhishek Singh]

Hi,

I am looking for 3'UTR region of ITPR2 gene (human) in pig. However this gene is not yet annotated but I am sure there must be a way around to get this sequence in pig.

What I have done till now is to extract 3'UTR region of ITPR2 for human and blast (nucleotide) and taken 82% match region in pig. I am not sure how good is this approach, could you please help me.

Thank you

Best regards

Abhishek Singh

[Cath Tyner]

Hello Abhishek

​,

​Thank you for submitting your question regarding finding specific annotation for the ITPR2 porcine gene. Although the ​gene has not been annotated in the reference assemblies native to the UCSC Genome Browser (

on ​

our latest susScr3 assembly, from GenBank accession ID: GCA_000003025.4), I went ahead and searched in other assemblies:

From NCBI, you can search the RefSeq assembly accession: GCF_000003025.5 (latest): https://www.ncbi.nlm.nih.gov/assembly/304498/

By clicking on "View the Genome" under the "Access the data" section.

Searching for "ITPR2" gives me a result of the entire chr5

​, so that gene is not annotated there either.​

I also searched our development hub for many genomes:

http://genome-test.cse.ucsc.edu/~hiram/hubs/genbank/vertebrate_mammalian/vertebrate_mammalian.ncbi.html

I also searched our Public Hubs hosted at UCSC Genome Browser:

Click on the "Public Hubs" tab and search for key words.

http://genome.ucsc.edu/cgi-bin/hgHubConnect

For any public hubs using porcine assemblies, such as "Porcine DNA methylation and gene transcription," you may want to load the hub and view the contact information; perhaps you can contact the group and ask for suggestions.

Meanwhile, 

​it is beyond the scope of this forum to provide research suggestions. However, you might be interested in using our LiftOver Tool or BLAT to compare regions in pig as you align them from human. Please note that these tools should used with special caution when comparing cross-species.

If our support team can be of further assistance in the use of those tools, please respond to this forum.

Please respond to this list if you have further questions!

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

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​Enjoy,​

Cath

. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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