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PCDH7 protocadherin 7 [ Homo sapiens (human) ]

Gene ID: 5099, updated on 2-Oct-2018

Summary

Official Symbol
PCDH7provided by HGNC
Official Full Name
protocadherin 7provided by HGNC
Primary source
HGNC:HGNC:8659
See related
Ensembl:ENSG00000169851 MIM:602988; Vega:OTTHUMG00000160364
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
BHPCDH; BH-Pcdh; PPP1R120
Summary
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The gene encodes a protein with an extracellular domain containing 7 cadherin repeats. The gene product is an integral membrane protein that is thought to function in cell-cell recognition and adhesion. Alternative splicing yields isoforms with unique cytoplasmic tails. [provided by RefSeq, Jul 2008]
Expression
Broad expression in brain (RPKM 10.8), spleen (RPKM 5.9) and 17 other tissues See more
Orthologs

Genomic context

See PCDH7 in Genome Data Viewer
Location:
4p15.1
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (30719861..31146801)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (30721951..31148423)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene cathepsin B pseudogene Neighboring gene ribosomal protein S3a pseudogene 17 Neighboring gene MT-CYB pseudogene 43 Neighboring gene long intergenic non-protein coding RNA 2497 Neighboring gene uncharacterized LOC105374564

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide screen for interactions reveals a new locus on 4p15 modifying the effect of waist-to-hip ratio on total cholesterol.
NHGRI GWA Catalog
Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies.
NHGRI GWA Catalog
Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
NHGRI GWA Catalog
Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults.
NHGRI GWA Catalog
Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
NHGRI GWA Catalog

Pathways from BioSystems

  • Hemostasis, organism-specific biosystem (from REACTOME)
    Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...
  • Platelet activation, signaling and aggregation, organism-specific biosystem (from REACTOME)
    Platelet activation, signaling and aggregation, organism-specific biosystemPlatelet activation begins with the initial binding of adhesive ligands and of the excitatory platelet agonists (released or generated at the sites of vascular trauma) to cognate receptors on the pla...
  • Platelet degranulation, organism-specific biosystem (from REACTOME)
    Platelet degranulation, organism-specific biosystemPlatelets function as exocytotic cells, secreting a plethora of effector molecules at sites of vascular injury. Platelets contain a number of distinguishable storage granules including alpha granules...
  • Response to elevated platelet cytosolic Ca2+, organism-specific biosystem (from REACTOME)
    Response to elevated platelet cytosolic Ca2+, organism-specific biosystemActivation of phospholipase C enzymes results in the generation of second messengers of the phosphatidylinositol pathway. The events resulting from this pathway are a rise in intracellular calcium an...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ97161

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
 
platelet degranulation TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
platelet alpha granule membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
protocadherin-7
Names
BH-protocadherin (brain-heart)
brain-heart protocadherin
protein phosphatase 1, regulatory subunit 120

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.

mRNA and Protein(s)

  1. NM_001173523.1NP_001166994.1  protocadherin-7 isoform d precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (d) represents the longest transcript and encodes the longest isoform (d).
    Source sequence(s)
    AC098595, AC107394, AC110766
    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  2. NM_002589.2NP_002580.2  protocadherin-7 isoform a precursor

    See identical proteins and their annotated locations for NP_002580.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a) uses an alternate splice pattern in the 3' CDS and 3' UTR, compared to variant d. The resulting isoform (a) has a shorter and distinct C-terminus, compared to isoform d.
    Source sequence(s)
    AC098595
    Consensus CDS
    CCDS33971.1
    UniProtKB/Swiss-Prot
    O60245
    Related
    ENSP00000355243.2, OTTHUMP00000218096, ENST00000361762.3, OTTHUMT00000360366
    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  3. NM_032456.2NP_115832.1  protocadherin-7 isoform b precursor

    See identical proteins and their annotated locations for NP_115832.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b) is intronless, compared to variant d. The resulting isoform (b) has a shorter and distinct C-terminus, compared to isoform d.
    Source sequence(s)
    AC098595
    Consensus CDS
    CCDS75116.1
    UniProtKB/Swiss-Prot
    O60245
    Related
    ENSP00000441802.2, OTTHUMP00000275692, ENST00000543491.2, OTTHUMT00000476518
    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  4. NM_032457.3NP_115833.2  protocadherin-7 isoform c precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (c) uses an alternate in-frame splice site in the 3' coding region, compared to variant d. The resulting isoform (c) lacks an internal segment near the C-terminus, compared to isoform d.
    Source sequence(s)
    AC098595, AC107394, AC110766
    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin

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.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    30719861..31146801
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513842.3XP_011512144.1  protocadherin-7 isoform X1

    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  2. XM_017008261.2XP_016863750.1  protocadherin-7 isoform X4

  3. XM_017008260.2XP_016863749.1  protocadherin-7 isoform X3

  4. XM_005248163.4XP_005248220.1  protocadherin-7 isoform X7

    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  5. XM_017008259.2XP_016863748.1  protocadherin-7 isoform X2

  6. XM_017008262.2XP_016863751.1  protocadherin-7 isoform X5

  7. XM_005248164.4XP_005248221.1  protocadherin-7 isoform X8

    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  8. XM_011513843.3XP_011512145.1  protocadherin-7 isoform X6

    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  9. XM_005248166.4XP_005248223.1  protocadherin-7 isoform X18

    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  10. XM_011513844.3XP_011512146.1  protocadherin-7 isoform X15

    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  11. XM_017008272.2XP_016863761.1  protocadherin-7 isoform X17

  12. XM_017008264.2XP_016863753.1  protocadherin-7 isoform X9

  13. XM_017008263.2XP_016863752.1  protocadherin-7 isoform X9

  14. XM_017008266.2XP_016863755.1  protocadherin-7 isoform X11

  15. XM_017008265.2XP_016863754.1  protocadherin-7 isoform X10

  16. XM_017008268.2XP_016863757.1  protocadherin-7 isoform X13

  17. XM_017008271.2XP_016863760.1  protocadherin-7 isoform X16

    Conserved Domains (2) summary
    cd11304
    Location:541635
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08374
    Location:8421053
    Protocadherin; Protocadherin
  18. XM_017008267.2XP_016863756.1  protocadherin-7 isoform X12

  19. XM_017008269.2XP_016863758.1  protocadherin-7 isoform X14

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