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Gene

USP9Y

ubiquitin specific peptidase 9 Y-linked

Summary

Cytogenetic location
Yq11.221
Coordinates
Chromosome Y: 12,701,231–12,860,839 (GRCh38)
Exons
46 exons across 159.6 kb
Protein
2,555 amino acids
Also known as
DFFRY, FAF-Y, AZFA
MANE Select transcript
ENST00000338981.7NM_004654.4
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated reports relevant to this gene

No Genome Test report reads USP9Y yet. The test sequences your whole genome, so your data includes it all the same.

How USP9Y is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome Y, with a bracket where USP9Y sits. USP9Y and 2 genes near it on chromosome Y, from 12,281,035 to 13,281,034.Chromosome YYq11.221p11.32p11.31p11.2p11.1q11.1q11.21q11.221q11.222q11.223q11.23q1212.4 Mb12.6 Mb12.8 Mb13 Mb13.2 MbUSP9Y: 12,701,231–12,860,839, forward strandUSP9YDDX3Y: 12,904,108–12,920,478, forward strandDDX3YUTY: 13,234,577–13,480,673, reverse strandUTYDiagram of USP9Y: 46 exons on the forward strand of chromosome YExon 36: 1 known disease-causing siteExon 1: 12,701,231–12,702,055, 825 basesExon 2: 12,708,634–12,708,693, 60 basesExon 3: 12,709,388–12,709,543, 156 basesExon 4: 12,720,589–12,720,737, 149 basesExon 5: 12,722,108–12,722,187, 80 basesExon 6: 12,725,113–12,725,225, 113 basesExon 7: 12,726,575–12,726,793, 219 basesExon 8: 12,735,612–12,735,727, 116 basesExon 9: 12,735,998–12,736,249, 252 basesExon 10: 12,736,411–12,736,549, 139 basesExon 11: 12,738,157–12,738,309, 153 basesExon 12: 12,739,525–12,739,629, 105 basesExon 13: 12,757,192–12,757,398, 207 basesExon 14: 12,758,506–12,758,642, 137 basesExon 15: 12,760,484–12,760,617, 134 basesExon 16: 12,771,068–12,771,155, 88 basesExon 17: 12,773,583–12,773,925, 343 basesExon 18: 12,775,471–12,775,566, 96 basesExon 19: 12,776,649–12,776,860, 212 basesExon 20: 12,778,019–12,778,259, 241 basesExon 21: 12,778,606–12,778,755, 150 basesExon 22: 12,779,526–12,779,646, 121 basesExon 23: 12,786,203–12,786,333, 131 basesExon 24: 12,786,522–12,786,800, 279 basesExon 25: 12,790,407–12,790,532, 126 basesExon 26: 12,791,499–12,791,624, 126 basesExon 27: 12,793,032–12,793,201, 170 basesExon 28: 12,810,179–12,810,287, 109 basesExon 29: 12,810,672–12,810,818, 147 basesExon 30: 12,811,635–12,811,781, 147 basesExon 31: 12,812,830–12,813,052, 223 basesExon 32: 12,816,124–12,816,344, 221 basesExon 33: 12,818,420–12,818,610, 191 basesExon 34: 12,833,688–12,833,861, 174 basesExon 35: 12,837,911–12,838,052, 142 basesExon 36: 12,839,864–12,840,614, 751 basesExon 37: 12,841,010–12,841,133, 124 basesExon 38: 12,842,240–12,842,465, 226 basesExon 39: 12,843,064–12,843,193, 130 basesExon 40: 12,846,333–12,846,518, 186 basesExon 41: 12,846,933–12,847,153, 221 basesExon 42: 12,847,239–12,847,327, 89 basesExon 43: 12,856,340–12,856,496, 157 basesExon 44: 12,856,633–12,856,845, 213 basesExon 45: 12,857,566–12,857,661, 96 basesExon 46: 12,859,279–12,860,839, 1,561 bases110203040465′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 10 kb of the gene's 159.6 kb; 7,668 of those bases code for the protein.

Sequencing USP9Y

1Low

How hard USP9Y is to sequence with short reads, out of 100

  • Mappability0%
  • Homology0%
  • Repeats2.4%
  • GC content4.6%
  • Reference coverage0%

1

position in USP9Y where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 159.6 kb of USP9Y, introns included, not only the 10 kb of exons.

Traits linked to USP9Y

The Human Phenotype Ontology lists these as features of the rare conditions USP9Y can cause. Each trait's page lists the other genes linked to it.

External links

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.17-8666dff2.

Cite this page

APA

Dante Labs. (n.d.). USP9Y gene: ubiquitin specific peptidase 9 Y-linked. Retrieved 17 October 2026, from https://dantelabs.com/genes/usp9y

Vancouver

Dante Labs. USP9Y gene: ubiquitin specific peptidase 9 Y-linked [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/usp9y

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