distribution of EXONS and INTRONS in a gene

[Khan, Qasim]

Dear Sir,

 

How could I obtain the distribution of exons and introns  in a gene, e.g., mouse sulfotransferase 1d1 gene, so that I could locate the position of the primer binding sites in that sequence. Please let me know if someone is familiar with that program.

 

Best regards,

Qasim A. Khan, Ph.D.

Department of Pharmacology,

Rosswellpark Cancer Institue

Buffa, NY 142081

Phone :716-845-8795

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[Jairo Navarro Gonzalez]

Hello Qasim,

Thank you for using the UCSC Genome Browser and your inquiry. I apologize for the delay in my response.

One of our engineers suggests that our Variant Annotation Integrator can provide information on whether your primer regions overlap with an exon or intron and provide other useful information such as the base position within the transcript. However, to use the Variant Annotation Integrator, you will need to convert these BED regions into a "fake" pgSnp - fake in the sense that the pgSnp file will not describe real variants, but instead merely list your regions of interest. You can find more information on the pgSnp file format at http://genome.ucsc.edu/FAQ/FAQformat.html#format10.

For example, Sult1d1 gene in mm10, I have saved a session with a custom track to represent a primer in the following region: chr5 87556853 87556875.
You can follow these steps to get information about where this primer overlaps:

1. Create a false pgSnp custom track, for example:

track type=pgSnp name="Sult1d1" 
chr5 87556853 87556875    -    1    0    0

2. Navigate to the custom track page and upload the pgSnp custom track from step 1.
3. After the custom track is uploaded, change the drop-down menu to view the custom track in the Variant Annotation Integrator and then click go.
4. On the Variant Annotation Integrator tool, select your custom track from the Select Variants menu.
5. In the Define Filters section, expand the Functional Role menu and then clear all of the boxes except for your regions of interest,

i.e. CDS - synonymous coding change, intron, or exon of a non-coding gene.

6. Click get results

You will now see information such as the primer's position in the cDNA, CDS, and the exon number. 

## ENSEMBL VARIANT EFFECT PREDICTOR format (UCSC Variant Annotation Integrator)
## Output produced at 2017-10-13 09:28:27
## Connected to UCSC database mm10
## Variants: Sult1d1 (customTrash.t1_genome_4413_f9c080)
## Transcripts: UCSC Genes (RefSeq, GenBank, tRNAs & Comparative Genomics) (mm10.knownGene)
## dbSNP: Simple Nucleotide Polymorphisms (dbSNP 142) (mm10.snp142)
Uploaded Variation    Location    Allele    Gene    Feature    Feature type    Consequence    Position in cDNA    Position in CDS    Position in protein    Amino acid change    Codon change    Co-located Variation    Extra
chr5_87556854_-    chr5:87556854-87556875    -    Sult1d1    uc008xyo.2    Transcript    frameshift_variant    973-994    754-775    252    VSPFM...RSEI*(45 aa)/EFQAIGRISSL*    GTGTCTCCTTTC...tcagagatctag(135 nt)/gaatttcaggcg...agttcactgtag(36 nt)    -    EXON=7/8

You can also search our mailing list archives for other previously asked questions. For example, you may also be interested in this previously answered question:

Is there an automated way to determine which primer pairs in a given set produce products that span exons?

You may also be interested in NCBI's Primer-BLAST tool to design primers:

https://www.ncbi.nlm.nih.gov/tools/primer-blast/

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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