Human Gene PCDHGA7 (uc003lka.2) Description and Page Index
  Description: Homo sapiens protocadherin gamma subfamily A, 7 (PCDHGA7), transcript variant 1, mRNA.
RefSeq Summary (NM_018920): This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr5:140,762,467-140,892,548 Size: 130,082 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr5:140,762,467-140,890,740 Size: 128,274 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:140,762,467-140,892,548)mRNA (may differ from genome)Protein (932 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: PCDG7_HUMAN
DESCRIPTION: RecName: Full=Protocadherin gamma-A7; Short=PCDH-gamma-A7; Flags: Precursor;
FUNCTION: Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein (By similarity).
SIMILARITY: Contains 6 cadherin domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PCDHGA7
CDC HuGE Published Literature: PCDHGA7
Positive Disease Associations: Lymphocytes
Related Studies:
  1. Lymphocytes
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.72 RPKM in Cells - Cultured fibroblasts
Total median expression: 29.94 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -671.851808-0.372 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002126 - Cadherin
IPR015919 - Cadherin-like
IPR020894 - Cadherin_CS
IPR013164 - Cadherin_N

Pfam Domains:
PF00028 - Cadherin domain
PF08266 - Cadherin-like
PF15974 - Cadherin C-terminal cytoplasmic tail, catenin-binding region
PF16492 - Cadherin cytoplasmic C-terminal

SCOP Domains:
49313 - Cadherin-like

ModBase Predicted Comparative 3D Structure on Q9Y5G6
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding

Biological Process:
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007267 cell-cell signaling
GO:0007399 nervous system development

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  KJ899225 - Synthetic construct Homo sapiens clone ccsbBroadEn_08619 PCDHGB3 gene, encodes complete protein.
AF152318 - Homo sapiens protocadherin gamma A1 (PCDH-gamma-A1) mRNA, complete cds.
AF152322 - Homo sapiens protocadherin gamma A2 (PCDH-gamma-A2) mRNA, complete cds.
AB208927 - Homo sapiens mRNA for protocadherin gamma subfamily A, 3 isoform 1 precursor variant protein.
BC167820 - Synthetic construct Homo sapiens clone IMAGE:100068210, MGC:195827 protocadherin gamma subfamily A, 3 (PCDHGA3) mRNA, encodes complete protein.
AF152509 - Homo sapiens PCDH-gamma-A3 gene, aberrantly spliced, mRNA sequence.
AF152323 - Homo sapiens protocadherin gamma A3 (PCDH-gamma-A3) mRNA, complete cds.
AF152330 - Homo sapiens protocadherin gamma B1 (PCDH-gamma-B1) mRNA, complete cds.
AB527386 - Synthetic construct DNA, clone: pF1KE0392, Homo sapiens PCDHGA4 gene for protocadherin gamma subfamily A, 4, without stop codon, in Flexi system.
BC152812 - Synthetic construct Homo sapiens clone IMAGE:100016081, MGC:184138 protocadherin gamma subfamily A, 4 (PCDHGA4) mRNA, encodes complete protein.
BC156730 - Synthetic construct Homo sapiens clone IMAGE:100062283, MGC:190229 protocadherin gamma subfamily A, 4 (PCDHGA4) mRNA, encodes complete protein.
AF152324 - Homo sapiens protocadherin gamma A4 (PCDH-gamma-A4) mRNA, complete cds.
AF152331 - Homo sapiens protocadherin gamma B2 (PCDH-gamma-B2) mRNA, complete cds.
AF152325 - Homo sapiens protocadherin gamma A5 (PCDH-gamma-A5) mRNA, complete cds.
BC150172 - Homo sapiens protocadherin gamma subfamily B, 3, mRNA (cDNA clone MGC:164749 IMAGE:40147143), complete cds.
AF152332 - Homo sapiens protocadherin gamma B3 (PCDH-gamma-B3) mRNA, complete cds.
AB209178 - Homo sapiens mRNA for protocadherin gamma subfamily A, 6 isoform 1 precursor variant protein.
BC146651 - Homo sapiens protocadherin gamma subfamily A, 6, mRNA (cDNA clone MGC:164778 IMAGE:40147340), complete cds.
AF152326 - Homo sapiens protocadherin gamma A6 (PCDH-gamma-A6) mRNA, complete cds.
LF211023 - JP 2014500723-A/18526: Polycomb-Associated Non-Coding RNAs.
AF152327 - Homo sapiens protocadherin gamma A7 (PCDH-gamma-A7) mRNA, complete cds.
AB208958 - Homo sapiens mRNA for protocadherin gamma subfamily A, 7 isoform 1 precursor variant protein.
AF152333 - Homo sapiens protocadherin gamma B4 (PCDH-gamma-B4) mRNA, complete cds.
MA446600 - JP 2018138019-A/18526: Polycomb-Associated Non-Coding RNAs.
LF212732 - JP 2014500723-A/20235: Polycomb-Associated Non-Coding RNAs.
BC136747 - Homo sapiens protocadherin gamma subfamily A, 7, mRNA (cDNA clone MGC:168360 IMAGE:9020737), complete cds.
BC136748 - Homo sapiens protocadherin gamma subfamily A, 7, mRNA (cDNA clone MGC:168361 IMAGE:9020738), complete cds.
KJ894308 - Synthetic construct Homo sapiens clone ccsbBroadEn_03702 PCDHGA7 gene, encodes complete protein.
AF152514 - Homo sapiens protocadherin gamma A7 short form protein (PCDH-gamma-A7) variable region sequence, complete cds.
LF343274 - JP 2014500723-A/150777: Polycomb-Associated Non-Coding RNAs.
LF343275 - JP 2014500723-A/150778: Polycomb-Associated Non-Coding RNAs.
LF343276 - JP 2014500723-A/150779: Polycomb-Associated Non-Coding RNAs.
LF343277 - JP 2014500723-A/150780: Polycomb-Associated Non-Coding RNAs.
LF343278 - JP 2014500723-A/150781: Polycomb-Associated Non-Coding RNAs.
LF343279 - JP 2014500723-A/150782: Polycomb-Associated Non-Coding RNAs.
LF343280 - JP 2014500723-A/150783: Polycomb-Associated Non-Coding RNAs.
MA578851 - JP 2018138019-A/150777: Polycomb-Associated Non-Coding RNAs.
MA578852 - JP 2018138019-A/150778: Polycomb-Associated Non-Coding RNAs.
MA578853 - JP 2018138019-A/150779: Polycomb-Associated Non-Coding RNAs.
MA578854 - JP 2018138019-A/150780: Polycomb-Associated Non-Coding RNAs.
MA578855 - JP 2018138019-A/150781: Polycomb-Associated Non-Coding RNAs.
MA578856 - JP 2018138019-A/150782: Polycomb-Associated Non-Coding RNAs.
MA578857 - JP 2018138019-A/150783: Polycomb-Associated Non-Coding RNAs.
MA448309 - JP 2018138019-A/20235: Polycomb-Associated Non-Coding RNAs.
BC160101 - Synthetic construct Homo sapiens clone IMAGE:100064133, MGC:193216 protocadherin gamma subfamily A, 8 (PCDHGA8) mRNA, encodes complete protein.
AF152328 - Homo sapiens protocadherin gamma A8 (PCDH-gamma-A8) mRNA, complete cds.
AB384865 - Synthetic construct DNA, clone: pF1KB3849, Homo sapiens PCDHGB5 gene for protocadherin gamma B5, complete cds, without stop codon, in Flexi system.
AF152334 - Homo sapiens protocadherin gamma B5 (PCDH-gamma-B5) mRNA, complete cds.
AF152329 - Homo sapiens protocadherin gamma A9 (PCDH-gamma-A9) mRNA, complete cds.
BC156637 - Synthetic construct Homo sapiens clone IMAGE:100062149, MGC:190181 protocadherin gamma subfamily B, 6 (PCDHGB6) mRNA, encodes complete protein.
AF152335 - Homo sapiens protocadherin gamma B6 (PCDH-gamma-B6) mRNA, complete cds.
AF152319 - Homo sapiens protocadherin gamma A10 (PCDH-gamma-A10) mRNA, complete cds.
BC051788 - Homo sapiens protocadherin gamma subfamily B, 7, mRNA (cDNA clone MGC:57549 IMAGE:4941167), complete cds.
AF152336 - Homo sapiens protocadherin gamma B7 (PCDH-gamma-B7) mRNA, complete cds.
AK026188 - Homo sapiens cDNA: FLJ22535 fis, clone HRC13115, highly similar to AF152336 Homo sapiens protocadherin gamma B7 (PCDH-gamma-B7) mRNA.
BC136781 - Homo sapiens protocadherin gamma subfamily A, 11, mRNA (cDNA clone MGC:168394 IMAGE:9020771), complete cds.
BC171774 - Homo sapiens protocadherin gamma subfamily A, 11, mRNA (cDNA clone MGC:198489 IMAGE:9054428), complete cds.
AF152504 - Homo sapiens protocadherin gamma A11 (PCDH-gamma-A11) mRNA, alternatively spliced, complete cds.
AF152320 - Homo sapiens protocadherin gamma A11 (PCDH-gamma-A11) mRNA, complete cds.
AB011160 - Homo sapiens KIAA0588 mRNA for KIAA0588 protein.
AB383915 - Synthetic construct DNA, clone: pF1KSDA0588, Homo sapiens PCDHGA12 gene for protocadherin gamma A12 precursor, complete cds, without stop codon, in Flexi system.
BC172309 - Synthetic construct Homo sapiens clone IMAGE:100069003, MGC:199014 protocadherin gamma subfamily A, 12 (PCDHGA12) mRNA, encodes complete protein.
AF152321 - Homo sapiens protocadherin gamma A12 (PCDH-gamma-A12) mRNA, complete cds.
BC006439 - Homo sapiens protocadherin gamma subfamily C, 3, mRNA (cDNA clone IMAGE:3010573), complete cds.
BC019299 - Homo sapiens protocadherin gamma subfamily C, 3, mRNA (cDNA clone MGC:4113 IMAGE:2905509), complete cds.
BC027451 - Homo sapiens protocadherin gamma subfamily C, 3, mRNA (cDNA clone IMAGE:4944432), complete cds.
L11373 - Human protocadherin 43 mRNA, complete cds for abbreviated PC43.
BC026218 - Homo sapiens protocadherin gamma subfamily C, 3, mRNA (cDNA clone MGC:21402 IMAGE:4153558), complete cds.
BC063437 - Homo sapiens protocadherin gamma subfamily C, 3, mRNA (cDNA clone IMAGE:5309650), complete cds.
CU675407 - Synthetic construct Homo sapiens gateway clone IMAGE:100018533 5' read PCDHGC3 mRNA.
DQ896354 - Synthetic construct Homo sapiens clone IMAGE:100010814; FLH193562.01L; RZPDo839H0768D protocadherin gamma subfamily C, 3 (PCDHGC3) gene, encodes complete protein.
DQ893469 - Synthetic construct clone IMAGE:100006099; FLH193566.01X; RZPDo839H0778D protocadherin gamma subfamily C, 3 (PCDHGC3) gene, encodes complete protein.
KJ891757 - Synthetic construct Homo sapiens clone ccsbBroadEn_01151 PCDHGC3 gene, encodes complete protein.
KJ897298 - Synthetic construct Homo sapiens clone ccsbBroadEn_06692 PCDHGC3 gene, encodes complete protein.
KJ905848 - Synthetic construct Homo sapiens clone ccsbBroadEn_15518 PCDHGC3 gene, encodes complete protein.
AF152337 - Homo sapiens protocadherin gamma C3 (PCDH-gamma-C3) mRNA, complete cds.
BC042650 - Homo sapiens protocadherin gamma subfamily C, 4, mRNA (cDNA clone IMAGE:4914375).
AF152338 - Homo sapiens protocadherin gamma C4 (PCDH-gamma-C4) mRNA, complete cds.
AF152339 - Homo sapiens protocadherin gamma C5 (PCDH-gamma-C5) mRNA, complete cds.
BC027470 - Homo sapiens protocadherin gamma subfamily C, 3, mRNA (cDNA clone IMAGE:4178411), complete cds.
BC004321 - Homo sapiens protocadherin gamma subfamily C, 3, mRNA (cDNA clone IMAGE:3628247), complete cds.
KJ901625 - Synthetic construct Homo sapiens clone ccsbBroadEn_11019 PCDHGC3 gene, encodes complete protein.
KJ905849 - Synthetic construct Homo sapiens clone ccsbBroadEn_15519 PCDHGC3 gene, encodes complete protein.
JD042738 - Sequence 23762 from Patent EP1572962.
JD339473 - Sequence 320497 from Patent EP1572962.
JD380555 - Sequence 361579 from Patent EP1572962.
JD096184 - Sequence 77208 from Patent EP1572962.
JD108747 - Sequence 89771 from Patent EP1572962.
JD142493 - Sequence 123517 from Patent EP1572962.
JD415722 - Sequence 396746 from Patent EP1572962.
JD120714 - Sequence 101738 from Patent EP1572962.
JD155678 - Sequence 136702 from Patent EP1572962.
JD217844 - Sequence 198868 from Patent EP1572962.
JD084034 - Sequence 65058 from Patent EP1572962.
JD350121 - Sequence 331145 from Patent EP1572962.
JD379856 - Sequence 360880 from Patent EP1572962.
JD075652 - Sequence 56676 from Patent EP1572962.
JD559925 - Sequence 540949 from Patent EP1572962.
JD038416 - Sequence 19440 from Patent EP1572962.
JD119706 - Sequence 100730 from Patent EP1572962.
JD208508 - Sequence 189532 from Patent EP1572962.
JD393401 - Sequence 374425 from Patent EP1572962.
JD471477 - Sequence 452501 from Patent EP1572962.
JD531171 - Sequence 512195 from Patent EP1572962.
JD349341 - Sequence 330365 from Patent EP1572962.
JD217972 - Sequence 198996 from Patent EP1572962.
JD241534 - Sequence 222558 from Patent EP1572962.
JD253747 - Sequence 234771 from Patent EP1572962.
JD402971 - Sequence 383995 from Patent EP1572962.
JD231320 - Sequence 212344 from Patent EP1572962.
JD273052 - Sequence 254076 from Patent EP1572962.
JD273053 - Sequence 254077 from Patent EP1572962.
JD335660 - Sequence 316684 from Patent EP1572962.
JD426818 - Sequence 407842 from Patent EP1572962.
JD074968 - Sequence 55992 from Patent EP1572962.
JD453230 - Sequence 434254 from Patent EP1572962.
JD094835 - Sequence 75859 from Patent EP1572962.
JD154991 - Sequence 136015 from Patent EP1572962.
JD389648 - Sequence 370672 from Patent EP1572962.
JD125298 - Sequence 106322 from Patent EP1572962.
JD195854 - Sequence 176878 from Patent EP1572962.
JD041525 - Sequence 22549 from Patent EP1572962.
JD239007 - Sequence 220031 from Patent EP1572962.
JD347391 - Sequence 328415 from Patent EP1572962.
JD404655 - Sequence 385679 from Patent EP1572962.
JD522875 - Sequence 503899 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RN87, NM_018920, NP_061743, PCDG7_HUMAN, Q9Y5D0, Q9Y5G6
UCSC ID: uc003lka.2
RefSeq Accession: NM_018920
Protein: Q9Y5G6 (aka PCDG7_HUMAN or CDG7_HUMAN)
CCDS: CCDS54927.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_018920.2
exon count: 4CDS single in 3' UTR: no RNA size: 4605
ORF size: 2799CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5169.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.