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

    Gene ID: 83259, updated on 2-Nov-2024

    Summary

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    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; AllianceGenome:HGNC:15813
    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

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    See PCDH11Y in Genome Data Viewer
    Location:
    Yp11.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (5000296..5742228)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (4679814..5422252)
    RS_2024_09 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 NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrY:4822044-4822666 Neighboring gene RNA, U2 small nuclear 57, pseudogene Neighboring gene voltage dependent anion channel 1 pseudogene 6 Neighboring gene NANOG hESC enhancer GRCh37_chrY:5192864-5193440 Neighboring gene eukaryotic translation initiation factor 4A1 pseudogene 2 Neighboring gene keratin 18 pseudogene 10 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrY:5577568-5578528 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. In the present study, PCDH11Yb, but not PCDH11Ya or PCDH11Yc, was expressed in germ cells isolated from the semen of all 13 men with proven fertility. However, in several subjects from various infertility classes, there was complete absence or a significant reduction in the expression of PCDH11Yb. In conclusion, expression levels of PCDH11Yb in germ cells in the semen were correlated with the fertility status of men.
      Title: Expression of protocadherin 11Yb (PCDH11Yb) in seminal germ cells is correlated with fertility status in men.
    2. PCDH11Y expression was detected in the fetal neocortex, ganglionic eminences, cerebellum, and inferior olive. In the adult brain, the cerebral cortex, hippocampal formation, and cerebellum and brain stem were immunoreactive.
      Title: Protocadherin 11X/Y a human-specific gene pair: an immunohistochemical survey of fetal and adult brains.
    3. the PCDH11X/Y gene pair determines cerebral asymmetry by initiating the right shift in Homo sapiens
      Title: The protocadherin 11X/Y (PCDH11X/Y) gene pair as determinant of cerebral asymmetry in modern Homo sapiens.
    4. Our data...extended the lack of association of late-onset Alzheimer's disease to common PCDH11Y variants.
      Title: Lack of association between protocadherin 11-X/Y (PCDH11X and PCDH11Y) polymorphisms and late onset Alzheimer's disease.
    5. The present article investigated the patterns of alternative splicing and expression of the PCDH11X/Y genes.
      Title: Quantitative analysis of alternative transcripts of human PCDH11X/Y genes.
    6. a candidate for the evolution of hominid-specific characteristics including the sexual dimorphism of cerebral asymmetry, a putative correlate of language
      Title: Accelerated evolution of Protocadherin11X/Y: a candidate gene-pair for cerebral asymmetry and language.
    7. This study provided the evidence for positive selection on Protocadherin Y gene in human lineage for schizophrenia.
      Title: Evidence for positive selection on Protocadherin Y gene in Homo sapiens: implications for schizophrenia.
    8. We consider that a stronger case can be mounted for the Protocadherin11X/Y gene pair located in the hominid specific Xq21.3/Yp11.2 region of homology that was generated by a duplication from the X
      Title: Where and what is the right shift factor or cerebral dominance gene? A critique of Francks et al. (2007).
    9. Findings do not support the role of PCDH11Y, or more generally of a frequent specific Y chromosome, in the susceptibility to these neuropsychiatric disorders.
      Title: Expression and genetic variability of PCDH11Y, a gene specific to Homo sapiens and candidate for susceptibility to psychiatric disorders.
    10. Our findings suggest a novel mechanism for the progression of CaP involving expression of PCDH-PC. This novel protocadherin induces Wnt signaling, promotes malignant behavior and hormone-resistance of CaP cells.
      Title: Protocadherin-PC promotes androgen-independent prostate cancer cell growth.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genetically distinct subsets within ANCA-associated vasculitis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of Wnt signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in spermatogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in sperm head IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in sperm midpiece IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    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
      5071..746999
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001278619.2 → NP_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/TrEMBL
      A8K0W1
      Related
      ENSP00000482115.1, ENST00000622698.4
      Conserved Domains (4) summary
      cd11304
      Location:493 → 587
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:405 → 485
      CA; Cadherin repeats
      pfam08374
      Location:796 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:49 → 123
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    2. NM_001395587.1 → NP_001382516.1  protocadherin-11 Y-linked isoform d

      Status: REVIEWED

      Source sequence(s)
      AC010081, AC010722, AC012067, AC012667
      Consensus CDS
      CCDS94706.1
      UniProtKB/TrEMBL
      A0A8V8TP37
      Related
      ENSP00000513983.1, ENST00000698851.1
      Conserved Domains (2) summary
      cd11304
      Location:412 → 506
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:324 → 404
      CA; Cadherin repeats

    3. NM_032971.3 → NP_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/TrEMBL
      A8K0W1
      Related
      ENSP00000330552.4, ENST00000333703.8
      Conserved Domains (4) summary
      cd11304
      Location:493 → 587
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:405 → 485
      CA; Cadherin repeats
      pfam08374
      Location:796 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:49 → 123
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    4. NM_032972.3 → NP_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/TrEMBL
      A8K0W1
      Related
      ENSP00000355419.5, ENST00000362095.9
      Conserved Domains (4) summary
      cd11304
      Location:504 → 598
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:416 → 496
      CA; Cadherin repeats
      pfam08374
      Location:807 → 1008
      Protocadherin; Protocadherin
      cl09101
      Location:60 → 134
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    5. NM_032973.2 → NP_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
      Q70LR6, Q70LS0, Q70LS1, Q70LS2, Q70LS3, Q70LS4, Q70LS5, Q8WY34, Q9BZA8, Q9BZA9, Q9H4E1
      Related
      ENSP00000383306.3, ENST00000400457.3
      Conserved Domains (5) summary
      cd11304
      Location:504 → 598
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:416 → 496
      CA; Cadherin repeats
      pfam08374
      Location:807 → 1008
      Protocadherin; Protocadherin
      pfam14650
      Location:1164 → 1270
      FAM75; FAM75 family
      cl09101
      Location:60 → 134
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

      Range
      5000296..5742228
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017030079.2 → XP_016885568.1  protocadherin-11 Y-linked isoform X1

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

    3. XM_017030080.2 → XP_016885569.1  protocadherin-11 Y-linked isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060948.1 Alternate T2T-CHM13v2.0

      Range
      4679814..5422252
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328379.1 → XP_054184354.1  protocadherin-11 Y-linked isoform X1

    2. XM_054328381.1 → XP_054184356.1  protocadherin-11 Y-linked isoform X1

    3. XM_054328380.1 → XP_054184355.1  protocadherin-11 Y-linked isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BZA8.1 GenPept UniProtKB/Swiss-Prot:Q9BZA8

    Gene LinkOut

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