Skip to content
Use your HSA or FSA funds
Sequence your genome (opens in a new tab)

Gene

PCDH11Y

protocadherin 11 Y-linked

Summary

Cytogenetic location
Yp11.2
Coordinates
Chromosome Y: 5,000,296–5,742,224 (GRCh38)
Exons
6 exons across 741.9 kb
Protein
1,248 amino acids
Also known as
PCDHY
Previous symbols
PCDH22
MANE Select transcript
ENST00000698851.1NM_001395587.1
Locus type
Protein-coding
  • Very high
  • Confident
  • Low
  • Very low

Curated reports relevant to this gene

No Genome Test report reads PCDH11Y yet. The test sequences your whole genome, so your data includes it all the same.

How PCDH11Y is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Stretches short reads find hard
Chromosome Y, with a bracket where PCDH11Y sits. PCDH11Y and 1 gene near it on chromosome Y, from 4,258,367 to 6,484,153.Chromosome YYp11.2p11.32p11.31p11.2p11.1q11.1q11.21q11.221q11.222q11.223q11.23q124.5 Mb5 Mb5.5 Mb6 MbPCDH11Y: 5,000,296–5,742,224, forward strandPCDH11YTSPY2: 6,246,223–6,249,020, forward strandTSPY2Diagram of PCDH11Y: 6 exons on the forward strand of chromosome YExon 1: 5,000,296–5,000,605, 310 basesExon 2: 5,056,889–5,057,459, 571 basesExon 3: 5,098,215–5,100,707, 2,493 basesExon 4: 5,501,057–5,501,255, 199 basesExon 5: 5,581,775–5,581,798, 24 basesExon 6: 5,737,272–5,742,224, 4,953 bases1234565′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 8.6 kb of the gene's 741.9 kb; 3,747 of those bases code for the protein.

Sequencing PCDH11Y

97Hard

How hard PCDH11Y is to sequence with short reads, out of 100

Much of PCDH11Y sits where short reads can miss or misplace a change.

What adds to it: the share of PCDH11Y's exons in each kind of hard region

  • Mappability93%
  • Homology100%
  • Shared with chrY0%
  • Reference coverage0%
  • Repeats4.9%
  • GC content12%

A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scored

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.
  • The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.

Cite this page

APA

Dante Labs. (n.d.). PCDH11Y gene: protocadherin 11 Y-linked. Retrieved 20 October 2026, from https://dantelabs.com/genes/pcdh11y

Vancouver

Dante Labs. PCDH11Y gene: protocadherin 11 Y-linked [Internet]. [cited 20 October 2026]. Available from: https://dantelabs.com/genes/pcdh11y

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test