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PCDH11Y protocadherin 11 Y-linked [ Homo sapiens (human) ]

Gene ID: 83259, updated on 25-Jul-2021

Summary

Official Symbol
PCDH11Yprovided by HGNC
Official Full Name
protocadherin 11 Y-linkedprovided by HGNC
Primary source
HGNC:HGNC:15813
See related
Ensembl:ENSG00000099715 MIM:400022
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PCDHX; PCDHY; PCDH22; PCDH-PC
Summary
This gene belongs to the protocadherin family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing seven cadherin repeats, a transmembrane domain, and a cytoplasmic tail that differs from those of the classical cadherins. This gene is located on the Y chromosome in a block of X/Y homology and is very closely related to its paralog on the X chromosome. The protein is thought to play a role in cell-cell recognition during development of the central nervous system. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
Expression
Biased expression in brain (RPKM 1.4), ovary (RPKM 0.6) and 5 other tissues See more
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Genomic context

See PCDH11Y in Genome Data Viewer
Location:
Yp11.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) Y NC_000024.10 (5000044..5742228)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (4868337..5610269)

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene microRNA 9985 Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 2 Neighboring gene RNA, U2 small nuclear 57, pseudogene Neighboring gene voltage dependent anion channel 1 pseudogene 6 Neighboring gene eukaryotic translation initiation factor 4A1 pseudogene 2 Neighboring gene keratin 18 pseudogene 10 Neighboring gene sorting nexin 3 pseudogene 1 Y-linked Neighboring gene ribosomal protein L26 pseudogene 37 Neighboring gene TUSC2 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genetically distinct subsets within ANCA-associated vasculitis.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
protocadherin-11 Y-linked
Names
protocadherin 22
protocadherin on the Y chromosome
protocadherin prostate cancer
protocadherin-PC

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011652.1 RefSeqGene

    Range
    60865..747003
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001278619.2NP_001265548.1  protocadherin-11 Y-linked isoform a

    See identical proteins and their annotated locations for NP_001265548.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (d, also known as Ty2) contains an alternate exon in the 5' UTR, compared to variant a. Variants a and d encode the same isoform (a).
    Source sequence(s)
    AC010722, AF277053, AJ276803
    Consensus CDS
    CCDS14776.1
    UniProtKB/Swiss-Prot
    Q9BZA8
    Related
    ENSP00000482115.1, ENST00000622698.4
    Conserved Domains (4) summary
    cd11304
    Location:493587
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:405485
    CA; Cadherin repeats
    pfam08374
    Location:796997
    Protocadherin; Protocadherin
    cl09101
    Location:49123
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  2. NM_001395587.1NP_001382516.1  protocadherin-11 Y-linked

    Status: REVIEWED

    Source sequence(s)
    AC010081, AC010722, AC012067, AC012667
  3. NM_032971.3NP_116753.1  protocadherin-11 Y-linked isoform a

    See identical proteins and their annotated locations for NP_116753.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a, also known as Ty1) represents the shortest transcript and encodes the shortest isoform (a). Variants a and d encode the same isoform (a).
    Source sequence(s)
    AC010722, AJ276803
    Consensus CDS
    CCDS14776.1
    UniProtKB/Swiss-Prot
    Q9BZA8
    Related
    ENSP00000330552.4, ENST00000333703.8
    Conserved Domains (4) summary
    cd11304
    Location:493587
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:405485
    CA; Cadherin repeats
    pfam08374
    Location:796997
    Protocadherin; Protocadherin
    cl09101
    Location:49123
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  4. NM_032972.3NP_116754.1  protocadherin-11 Y-linked isoform b precursor

    See identical proteins and their annotated locations for NP_116754.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b, also known as Ty4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant a. The encoded isoform (b) is longer and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AC010722, AF332216, AJ276803
    Consensus CDS
    CCDS14777.1
    UniProtKB/Swiss-Prot
    Q9BZA8
    Related
    ENSP00000355419.5, ENST00000362095.9
    Conserved Domains (4) summary
    cd11304
    Location:504598
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:416496
    CA; Cadherin repeats
    pfam08374
    Location:8071008
    Protocadherin; Protocadherin
    cl09101
    Location:60134
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  5. NM_032973.2NP_116755.1  protocadherin-11 Y-linked isoform c precursor

    See identical proteins and their annotated locations for NP_116755.1

    Status: REVIEWED

    Source sequence(s)
    AF332217, AJ564971
    Consensus CDS
    CCDS76066.1
    UniProtKB/Swiss-Prot
    Q9BZA8
    UniProtKB/TrEMBL
    Q70LR4
    Related
    ENSP00000383306.3, ENST00000400457.3
    Conserved Domains (5) summary
    cd11304
    Location:504598
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:416496
    CA; Cadherin repeats
    pfam08374
    Location:8071008
    Protocadherin; Protocadherin
    pfam14650
    Location:11641270
    FAM75; FAM75 family
    cl09101
    Location:60134
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p13 Primary Assembly

    Range
    5000044..5742228
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017030079.1XP_016885568.1  protocadherin-11 Y-linked isoform X1

  2. XM_017030081.1XP_016885570.1  protocadherin-11 Y-linked isoform X1

  3. XM_017030080.1XP_016885569.1  protocadherin-11 Y-linked isoform X1

  4. XM_017030082.1XP_016885571.1  protocadherin-11 Y-linked isoform X2

    UniProtKB/Swiss-Prot
    Q9BZA8
    Conserved Domains (4) summary
    cd11304
    Location:493587
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:405485
    CA; Cadherin repeats
    pfam08374
    Location:796997
    Protocadherin; Protocadherin
    cl09101
    Location:49123
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  5. XM_017030083.1XP_016885572.1  protocadherin-11 Y-linked isoform X3

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