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PCDH11X protocadherin 11 X-linked [ Homo sapiens (human) ]

Gene ID: 27328, updated on 11-Sep-2019

Summary

Official Symbol
PCDH11Xprovided by HGNC
Official Full Name
protocadherin 11 X-linkedprovided by HGNC
Primary source
HGNC:HGNC:8656
See related
Ensembl:ENSG00000102290 MIM:300246
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; PCDH-X; PCDH-Y; PCDH11; PCDH22; PCDH11Y; PPP1R119
Summary
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing 7 cadherin repeats, a transmembrane domain and a cytoplasmic tail that differs from those of the classical cadherins. The gene is located in a major X/Y block of homology and its Y homolog, despite divergence leading to coding region changes, is the most closely related cadherin family member. The protein is thought to play a fundamental role in cell-cell recognition essential for the segmental development and function of the central nervous system. Disruption of this gene may be associated with developmental dyslexia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
Expression
Biased expression in ovary (RPKM 3.1), brain (RPKM 2.5) and 2 other tissues See more
Orthologs

Genomic context

See PCDH11X in Genome Data Viewer
Location:
Xq21.31
Exon count:
15
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (91779310..92623230)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (91034260..91878229)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 4 Neighboring gene uncharacterized LOC105373293 Neighboring gene RNA, U2 small nuclear 26, pseudogene Neighboring gene voltage dependent anion channel 1 pseudogene 3 Neighboring gene eukaryotic translation initiation factor 4A1 pseudogene 10 Neighboring gene keratin 18 pseudogene 11 Neighboring gene sorting nexin 3 pseudogene 1 X-linked Neighboring gene ribosomal protein L26 pseudogene 36 Neighboring gene TUSC2 pseudogene 2

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

NHGRI GWAS Catalog

Description
Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease.
NHGRI GWA Catalog
Genetically distinct subsets within ANCA-associated vasculitis.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
negative regulation of phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
protocadherin-11 X-linked
Names
Protocadherin on the Y chromosome
Protocadherin prostate cancer
Protocadherin-11 Y-linked
Protocadherin-22
Protocadherin-PC
protein phosphatase 1, regulatory subunit 119
protocadherin 11X
protocadherin on the X chromosome
protocadherin-S

NCBI Reference Sequences (RefSeq)

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_016251.1 RefSeqGene

    Range
    61201..848970
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001168360.1NP_001161832.1  protocadherin-11 X-linked isoform e precursor

    See identical proteins and their annotated locations for NP_001161832.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (e) lacks an in-frame exon in the 3' coding region, compared to variant c. The encoded isoform (e) is shorter, compared to isoform c.
    Source sequence(s)
    AB037747, AJ564931, AJ564945, AY861432, BQ184367
    Consensus CDS
    CCDS55459.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000384758.1, ENST00000406881.3
    Conserved Domains (5) summary
    cd11304
    Location:253351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    CA; Cadherin repeats
    pfam08374
    Location:775976
    Protocadherin; Protocadherin
    pfam14650
    Location:11991269
    FAM75; FAM75 family
    cl09101
    Location:28102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  2. NM_001168361.1NP_001161833.1  protocadherin-11 X-linked isoform f precursor

    See identical proteins and their annotated locations for NP_001161833.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (f) lacks one exon and contains an alternate exon, which results in a frameshift and an early stop codon, compared to variant c. The encoded isoform (f) has a shorter and distinct C-terminus, compared to isoform c.
    Source sequence(s)
    AJ564931, AJ564945, AY861435, BQ184367
    Consensus CDS
    CCDS55458.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000423762.1, ENST00000504220.6
    Conserved Domains (4) summary
    cd11304
    Location:253351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    CA; Cadherin repeats
    pfam08374
    Location:775976
    Protocadherin; Protocadherin
    cl09101
    Location:28102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  3. NM_001168362.1NP_001161834.1  protocadherin-11 X-linked isoform g precursor

    See identical proteins and their annotated locations for NP_001161834.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (g) lacks two consecutive in-frame exons in the central coding region, compared to variant c. The encoded isoform (g) is shorter, compared to isoform c.
    Source sequence(s)
    AB037747, AJ564931, AJ564945, AY861433, BQ184367
    Consensus CDS
    CCDS55461.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000362180.1, ENST00000373088.5
    Conserved Domains (5) summary
    cd11304
    Location:253351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    CA; Cadherin repeats
    pfam08374
    Location:775976
    Protocadherin; Protocadherin
    pfam14650
    Location:11701240
    FAM75; FAM75 family
    cl09101
    Location:28102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  4. NM_001168363.1NP_001161835.1  protocadherin-11 X-linked isoform h precursor

    See identical proteins and their annotated locations for NP_001161835.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (h) lacks two in-frame exons in the central coding region, compared to variant c. The encoded isoform (h) is shorter, compared to isoform c.
    Source sequence(s)
    AB037747, AJ564931, AJ564945, AY861434, BQ184367
    Consensus CDS
    CCDS55460.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000355105.2, ENST00000361655.6
    Conserved Domains (5) summary
    cd11304
    Location:253351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    CA; Cadherin repeats
    pfam08374
    Location:775976
    Protocadherin; Protocadherin
    pfam14650
    Location:11891259
    FAM75; FAM75 family
    cl09101
    Location:28102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  5. NM_032968.4NP_116750.1  protocadherin-11 X-linked isoform c precursor

    See identical proteins and their annotated locations for NP_116750.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (c) represents the longest transcript and encodes the longest isoform (c).
    Source sequence(s)
    AF332218, AJ564945, BQ184367
    Consensus CDS
    CCDS14461.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000362186.1, ENST00000373094.5
    Conserved Domains (5) summary
    cd11304
    Location:253351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    CA; Cadherin repeats
    pfam08374
    Location:775976
    Protocadherin; Protocadherin
    pfam14650
    Location:12071277
    FAM75; FAM75 family
    cl09101
    Location:28102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  6. NM_032969.4NP_116751.1  protocadherin-11 X-linked isoform d precursor

    See identical proteins and their annotated locations for NP_116751.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (d) lacks an in-frame exon in the central coding region, compared to variant c. The encoded isoform (d) is shorter, compared to isoform c.
    Source sequence(s)
    AF332219, AJ564945, BQ184367
    Consensus CDS
    CCDS14462.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000362189.1, ENST00000373097.5
    Conserved Domains (5) summary
    cd11304
    Location:253351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    CA; Cadherin repeats
    pfam08374
    Location:775976
    Protocadherin; Protocadherin
    pfam14650
    Location:11971267
    FAM75; FAM75 family
    cl09101
    Location:28102
    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 Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    91779310..92623230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011530911.2XP_011529213.1  protocadherin-11 X-linked isoform X2

    See identical proteins and their annotated locations for XP_011529213.1

    Conserved Domains (5) summary
    cd11304
    Location:282380
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:413493
    CA; Cadherin repeats
    pfam08374
    Location:8041005
    Protocadherin; Protocadherin
    pfam14650
    Location:12361306
    FAM75; FAM75 family
    cl09101
    Location:57131
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  2. XM_017029417.1XP_016884906.1  protocadherin-11 X-linked isoform X2

    Conserved Domains (5) summary
    cd11304
    Location:282380
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:413493
    CA; Cadherin repeats
    pfam08374
    Location:8041005
    Protocadherin; Protocadherin
    pfam14650
    Location:12361306
    FAM75; FAM75 family
    cl09101
    Location:57131
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  3. XM_011530912.2XP_011529214.1  protocadherin-11 X-linked isoform X3

    Conserved Domains (5) summary
    cd11304
    Location:282380
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:413493
    CA; Cadherin repeats
    pfam08374
    Location:8041005
    Protocadherin; Protocadherin
    pfam14650
    Location:12281298
    FAM75; FAM75 family
    cl09101
    Location:57131
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  4. XM_017029418.1XP_016884907.1  protocadherin-11 X-linked isoform X4

  5. XM_011530913.2XP_011529215.1  protocadherin-11 X-linked isoform X5

    Conserved Domains (5) summary
    cd11304
    Location:282380
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:413493
    CA; Cadherin repeats
    pfam08374
    Location:8041005
    Protocadherin; Protocadherin
    pfam14650
    Location:12181288
    FAM75; FAM75 family
    cl09101
    Location:57131
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  6. XM_017029420.1XP_016884909.1  protocadherin-11 X-linked isoform X8

  7. XM_011530914.2XP_011529216.1  protocadherin-11 X-linked isoform X6

    See identical proteins and their annotated locations for XP_011529216.1

    UniProtKB/Swiss-Prot
    Q9BZA7
    Conserved Domains (5) summary
    cd11304
    Location:253351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    CA; Cadherin repeats
    pfam08374
    Location:775976
    Protocadherin; Protocadherin
    pfam14650
    Location:12071277
    FAM75; FAM75 family
    cl09101
    Location:28102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  8. XM_011530915.2XP_011529217.1  protocadherin-11 X-linked isoform X10

    See identical proteins and their annotated locations for XP_011529217.1

    Conserved Domains (4) summary
    cd11304
    Location:603698
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:413493
    CA; Cadherin repeats
    pfam08374
    Location:8041005
    Protocadherin; Protocadherin
    cl09101
    Location:57131
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  9. XM_017029422.1XP_016884911.1  protocadherin-11 X-linked isoform X11

    UniProtKB/Swiss-Prot
    Q9BZA7
    Conserved Domains (4) summary
    cd11304
    Location:253351
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    CA; Cadherin repeats
    pfam08374
    Location:775976
    Protocadherin; Protocadherin
    cl09101
    Location:28102
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  10. XM_011530910.1XP_011529212.1  protocadherin-11 X-linked isoform X2

    See identical proteins and their annotated locations for XP_011529212.1

    Conserved Domains (5) summary
    cd11304
    Location:282380
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:413493
    CA; Cadherin repeats
    pfam08374
    Location:8041005
    Protocadherin; Protocadherin
    pfam14650
    Location:12361306
    FAM75; FAM75 family
    cl09101
    Location:57131
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  11. XM_011530916.2XP_011529218.1  protocadherin-11 X-linked isoform X10

    See identical proteins and their annotated locations for XP_011529218.1

    Conserved Domains (4) summary
    cd11304
    Location:603698
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:413493
    CA; Cadherin repeats
    pfam08374
    Location:8041005
    Protocadherin; Protocadherin
    cl09101
    Location:57131
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
  12. XM_017029416.1XP_016884905.1  protocadherin-11 X-linked isoform X1

  13. XM_017029419.1XP_016884908.1  protocadherin-11 X-linked isoform X7

  14. XM_017029421.1XP_016884910.1  protocadherin-11 X-linked isoform X9

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_014522.1: Suppressed sequence

    Description
    NM_014522.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
  2. NM_032967.2: Suppressed sequence

    Description
    NM_032967.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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