Help about paralogous gene pairs (only human paralogous gene pairs)

[Chen Weizhong]

Dear scientist of UCSC Genome Browser,

May I ask some questions about human paralogous genes?

(1) Are there any tables of human paralogous genes/transcripts (pairs of human genes/transcripts having highly similar sequences) could be found in UCSC genome browser web portal?

Such as:

gene_1    gene_2    score

gene_3    gene_4    scorec

gene_5    gene_6    score

...

(2) Alternatively, are there any tables for pairs of similar sequences (of which their length is at about gene/transcript level) could be found in UCSC genome browser web portal?

Such as:

Chrom_A1    Start_A1    End_A1    Strand_A1    Chrom_B1    Start_B1    End_B1    Strand_B1    Score

Chrom_A2    Start_A2    End_A2    Strand_A2    Chrom_B2    Start_B2    End_B2    Strand_B2    Score

Chrom_A3    Start_A3    End_A3    Strand_A3    Chrom_B3    Start_B3    End_B3    Strand_B3    Score

...

Best,

Weizhong Chen, Ph.D

Staff scientist,

3D Biomedicine Science & Technology Co., Limited

Shanghai, China

[Matthew Speir]

Hello, Weizhong.

Thank you for your question about obtaining paralogous genes from the UCSC Genome Browser.

We do not have this information in our database, however, you may be interested in our Segmental Duplications track that shows regions of the genome with over 90% similar: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=genomicSuperDups. You could potentially do some filtering of these duplications by length to look for those that may contain paralogous genes.

Other sources of paralogs could be found through NCBI's BLASTP, https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins, or Ensembl's Biomart database, http://uswest.ensembl.org/Help/View?id=136.

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.

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Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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