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

Gene ID: 27328, updated on 12-Apr-2014
Official Symbol
PCDH11Xprovided by HGNC
Official Full Name
protocadherin 11 X-linkedprovided by HGNC
Primary source
HGNC:8656
Locus tag
RP13-138P15.1
See related
Ensembl:ENSG00000102290; HPRD:02215; MIM:300246; Vega:OTTHUMG00000021965
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; PCDH11
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. Transcripts arising from alternative splicing encode isoforms with variable cytoplasmic domains. [provided by RefSeq, Jul 2008]
Location :
Xq21.3
Sequence :
Chromosome: X; NC_000023.11 (91779261..92623230)
See PCDH11X in Epigenomics, MapViewer

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene poly(A) binding protein, cytoplasmic 5 Neighboring gene SERPINE1 mRNA binding protein 1 pseudogene 4 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 adaptor-related protein complex 2, beta 1 subunit pseudogene

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

Replication interactions

Interaction Pubs
Knockdown of protocadherin 11 X-linked (PCDH11X) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Protein Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

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
homophilic cell adhesion 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 TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
PubMed 
Preferred Names
protocadherin-11 X-linked
Names
protocadherin-11 X-linked
protocadherin-S
protocadherin 11X
protocadherin on the X chromosome

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
    5001..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 proteins identical to NP_001161832.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (e) has a shorter 5' UTR and differs in the 3' UTR and 3' coding region, compared to variant a. The resulting isoform (e) has a longer and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AB037747, AJ564931, AJ564945, AY861432, BQ184367
    Consensus CDS
    CCDS55459.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Conserved Domains (5) summary
    pfam08374
    Location:775999
    Blast Score: 675
    Protocadherin; Protocadherin
    cd11304
    Location:253351
    Blast Score: 311
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    Blast Score: 155
    CA; Cadherin repeats
    pfam14650
    Location:11631240
    Blast Score: 97
    FAM75; FAM75 family
    cl15786
    Location:28112
    Blast Score: 118
    CA_like; Cadherin repeat-like domain
  2. NM_001168361.1NP_001161833.1  protocadherin-11 X-linked isoform f precursor

    See proteins identical to NP_001161833.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (f) has a shorter 5' UTR and differs in the 3' UTR and 3' coding region, compared to variant a. The resulting isoform (f) has a longer and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AJ564931, AJ564945, AY861435, BQ184367
    Consensus CDS
    CCDS55458.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Conserved Domains (4) summary
    pfam08374
    Location:775976
    Blast Score: 688
    Protocadherin; Protocadherin
    cd11304
    Location:253351
    Blast Score: 304
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    Blast Score: 151
    CA; Cadherin repeats
    cl15786
    Location:28112
    Blast Score: 117
    CA_like; Cadherin repeat-like domain
  3. NM_001168362.1NP_001161834.1  protocadherin-11 X-linked isoform g precursor

    See proteins identical to NP_001161834.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (g) has a shorter 5' UTR and differs in the 3' UTR and 3' coding region, compared to variant a. The resulting isoform (g) has a longer and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AB037747, AJ564931, AJ564945, AY861433, BQ184367
    Consensus CDS
    CCDS55461.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Conserved Domains (5) summary
    pfam08374
    Location:775999
    Blast Score: 676
    Protocadherin; Protocadherin
    cd11304
    Location:253351
    Blast Score: 310
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    Blast Score: 155
    CA; Cadherin repeats
    pfam14650
    Location:11341211
    Blast Score: 98
    FAM75; FAM75 family
    cl15786
    Location:28112
    Blast Score: 118
    CA_like; Cadherin repeat-like domain
  4. NM_001168363.1NP_001161835.1  protocadherin-11 X-linked isoform h precursor

    See proteins identical to NP_001161835.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (h) has a shorter 5' UTR and differs in the 3' UTR and 3' coding region, compared to variant a. The resulting isoform (h) has a longer and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AB037747, AJ564931, AJ564945, AY861434, BQ184367
    Consensus CDS
    CCDS55460.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Conserved Domains (5) summary
    pfam08374
    Location:775999
    Blast Score: 676
    Protocadherin; Protocadherin
    cd11304
    Location:253351
    Blast Score: 310
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    Blast Score: 155
    CA; Cadherin repeats
    pfam14650
    Location:11531230
    Blast Score: 97
    FAM75; FAM75 family
    cl15786
    Location:28112
    Blast Score: 118
    CA_like; Cadherin repeat-like domain
  5. NM_014522.1NP_055337.1  protocadherin-11 X-linked isoform a precursor

    See proteins identical to NP_055337.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a) represents the shortest transcript and encodes the shortest isoform (a).
    Source sequence(s)
    AB026187
    Consensus CDS
    CCDS14464.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000355040, OTTHUMP00000023643, ENST00000361724, OTTHUMT00000057439
    Conserved Domains (4) summary
    pfam08374
    Location:775976
    Blast Score: 691
    Protocadherin; Protocadherin
    cd11304
    Location:574669
    Blast Score: 301
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    Blast Score: 150
    CA; Cadherin repeats
    cl15786
    Location:28112
    Blast Score: 116
    CA_like; Cadherin repeat-like domain
  6. NM_032967.2NP_116749.1  protocadherin-11 X-linked isoform b precursor

    See proteins identical to NP_116749.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b) differs in the 5' UTR, 3' UTR, and 3' coding region, compared to variant a. The resulting isoform (b) has a longer and distinct C-terminus, compared to isoform a. This variant contains an upstream in-frame start codon, but this upstream start codon has a weaker Kozak signal and would result in a protein that is 29 aa longer at the N-terminus and lacks a predicted signal peptide. The downstream translational start codon, as used in variant a, is selected for this RefSeq based on its better conservation in mammalian species, strong Kozak signal and on the presence of a predicted signal peptide in the protein N-terminus. Leaky scanning by ribosomes may allow translation initiation at the downstream start codon.
    Source sequence(s)
    AJ276804, DC350976
    Consensus CDS
    CCDS14463.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000378746, OTTHUMP00000023644, ENST00000395337, OTTHUMT00000057440
    Conserved Domains (4) summary
    pfam08374
    Location:775976
    Blast Score: 690
    Protocadherin; Protocadherin
    cd11304
    Location:253351
    Blast Score: 301
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    Blast Score: 150
    CA; Cadherin repeats
    cl15786
    Location:28112
    Blast Score: 116
    CA_like; Cadherin repeat-like domain
  7. NM_032968.3NP_116750.1  protocadherin-11 X-linked isoform c precursor

    See proteins identical to NP_116750.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (c) differs in the 3' UTR and 3' coding region, compared to variant a. The resulting isoform (c) has a longer and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AF332218, AJ564945, BQ184367
    Consensus CDS
    CCDS14461.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000362186, OTTHUMP00000023640, ENST00000373094, OTTHUMT00000057436
    Conserved Domains (5) summary
    pfam08374
    Location:775999
    Blast Score: 675
    Protocadherin; Protocadherin
    cd11304
    Location:253351
    Blast Score: 312
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    Blast Score: 156
    CA; Cadherin repeats
    pfam14650
    Location:11711248
    Blast Score: 97
    FAM75; FAM75 family
    cl15786
    Location:28112
    Blast Score: 118
    CA_like; Cadherin repeat-like domain
  8. NM_032969.3NP_116751.1  protocadherin-11 X-linked isoform d precursor

    See proteins identical to NP_116751.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (d) differs in the 3' UTR and 3' coding region, compared to variant a. The resulting isoform (c) has a longer and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AF332219, AJ564945, BQ184367
    Consensus CDS
    CCDS14462.1
    UniProtKB/Swiss-Prot
    Q9BZA7
    Related
    ENSP00000362189, OTTHUMP00000023641, ENST00000373097, OTTHUMT00000057437
    Conserved Domains (5) summary
    pfam08374
    Location:775999
    Blast Score: 676
    Protocadherin; Protocadherin
    cd11304
    Location:253351
    Blast Score: 311
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:384464
    Blast Score: 155
    CA; Cadherin repeats
    pfam14650
    Location:11611238
    Blast Score: 97
    FAM75; FAM75 family
    cl15786
    Location:28112
    Blast Score: 118
    CA_like; Cadherin repeat-like domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38 Primary Assembly

    Range
    91779261..92623230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. NW_001840475.1 Alternate HuRef

    Range
    1..1589
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018934.2 Alternate CHM1_1.1

    Range
    90926941..91771164
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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