Human Gene PCDHGA9 (ENST00000573521.2) from GENCODE V44
  Description: Homo sapiens protocadherin gamma subfamily A, 9 (PCDHGA9), transcript variant 1, mRNA. (from RefSeq NM_018921)
RefSeq Summary (NM_018921): 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].
Gencode Transcript: ENST00000573521.2
Gencode Gene: ENSG00000261934.3
Transcript (Including UTRs)
   Position: hg38 chr5:141,402,778-141,512,975 Size: 110,198 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr5:141,402,953-141,511,173 Size: 108,221 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:141,402,778-141,512,975)mRNA (may differ from genome)Protein (932 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHGNC
HPRDMalacardsMGIneXtProtOMIMPubMed
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PCDG9_HUMAN
DESCRIPTION: RecName: Full=Protocadherin gamma-A9; Short=PCDH-gamma-A9; 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.

-  Primer design for this transcript
 

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 2.91 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 55.89 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -40.40175-0.231 Picture PostScript Text
3' UTR -644.501802-0.358 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

ModBase Predicted Comparative 3D Structure on Q9Y5G4
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
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
  KJ894307 - Synthetic construct Homo sapiens clone ccsbBroadEn_03701 PCDHGA9 gene, encodes complete protein.
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.
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.
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.
BC132769 - Homo sapiens protocadherin gamma subfamily A, 9, mRNA (cDNA clone MGC:164400 IMAGE:40146791), complete cds.
AF152516 - Homo sapiens protocadherin gamma A9 short form protein (PCDH-gamma-A9) variable region sequence, complete cds.
HQ258519 - Synthetic construct Homo sapiens clone IMAGE:100072948 Unknown protein gene, encodes complete protein.
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: A2RU65, ENST00000573521.1, NM_018921, PCDG9_HUMAN, Q9Y5C9, Q9Y5G4, uc003lkh.1, uc003lkh.2, uc003lkh.3, uc003lkh.4
UCSC ID: ENST00000573521.2
RefSeq Accession: NM_018921
Protein: Q9Y5G4 (aka PCDG9_HUMAN or CDG9_HUMAN)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.