Human Gene PCDHA7 (ENST00000525929.1) from GENCODE V47lift37
  Description: Calcium-dependent cell-adhesion protein involved in cells self-recognition and non-self discrimination. Thereby, it is involved in the establishment and maintenance of specific neuronal connections in the brain. (from UniProt Q9UN72)
Gencode Transcript: ENST00000525929.1
Gencode Gene: ENSG00000204963.4
Transcript (Including UTRs)
   Position: hg19 chr5:140,213,969-140,391,929 Size: 177,961 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr5:140,213,969-140,389,522 Size: 175,554 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:140,213,969-140,391,929)mRNA (may differ from genome)Protein (937 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PCDA7_HUMAN
DESCRIPTION: RecName: Full=Protocadherin alpha-7; Short=PCDH-alpha-7; 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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Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.82 RPKM in Testis
Total median expression: 6.30 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
3' UTR -585.102407-0.243 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

SCOP Domains:
49313 - Cadherin-like

ModBase Predicted Comparative 3D Structure on Q9UN72
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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 DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding
GO:0042802 identical protein binding
GO:0046872 metal 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
GO:0009988 cell-cell recognition

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
  AB384778 - Synthetic construct DNA, clone: pF1KB3294, Homo sapiens PCDHA1 gene for protocadherin alpha 1 precursor, complete cds, without stop codon, in Flexi system.
AF169695 - Homo sapiens protocadherin alpha 1 alternate isoform (PCDH-alpha1) mRNA, complete cds.
AF152305 - Homo sapiens protocadherin alpha 1 (PCDH-alpha1) mRNA, complete cds.
BC166697 - Synthetic construct Homo sapiens clone IMAGE:100066423, MGC:195560 protocadherin alpha 1 (PCDHA1) mRNA, encodes complete protein.
AF152310 - Homo sapiens protocadherin alpha 2 (PCDH-alpha2) mRNA, complete cds.
AF152311 - Homo sapiens protocadherin alpha 3 (PCDH-alpha3) mRNA, complete cds.
AB208925 - Homo sapiens mRNA for protocadherin alpha 4 isoform 1 precursor variant protein.
AF152312 - Homo sapiens protocadherin alpha 4 (PCDH-alpha4) mRNA, complete cds.
BC033735 - Homo sapiens protocadherin alpha 5, mRNA (cDNA clone MGC:44897 IMAGE:5175471), complete cds.
AF152313 - Homo sapiens protocadherin alpha 5 (PCDH-alpha5) mRNA, complete cds.
AB208863 - Homo sapiens mRNA for protocadherin alpha 5 isoform 1 precursor variant protein.
BC036674 - Homo sapiens protocadherin alpha 6, mRNA (cDNA clone MGC:33675 IMAGE:5263226), complete cds.
AF169694 - Homo sapiens protocadherin alpha 6 alternate isoform (PCDH-alpha6) mRNA, complete cds.
KJ901067 - Synthetic construct Homo sapiens clone ccsbBroadEn_10461 PCDHA6-like gene, encodes complete protein.
AF152314 - Homo sapiens protocadherin alpha 6 (PCDH-alpha6) mRNA, complete cds.
AB209205 - Homo sapiens mRNA for protocadherin alpha 6 isoform 2 precursor variant protein.
AB527331 - Synthetic construct DNA, clone: pF1KE0061, Homo sapiens PCDHA7 gene for protocadherin alpha 7, without stop codon, in Flexi system.
BC148656 - Synthetic construct Homo sapiens clone IMAGE:100015585, MGC:183108 protocadherin alpha 7 (PCDHA7) mRNA, encodes complete protein.
BC156820 - Synthetic construct Homo sapiens clone IMAGE:100062561, MGC:190561 protocadherin alpha 7 (PCDHA7) mRNA, encodes complete protein.
BC156893 - Synthetic construct Homo sapiens clone IMAGE:100062695, MGC:190588 protocadherin alpha 7 (PCDHA7) mRNA, encodes complete protein.
AF152315 - Homo sapiens protocadherin alpha 7 (PCDH-alpha7) mRNA, complete cds.
AF152316 - Homo sapiens protocadherin alpha 8 (PCDH-alpha8) mRNA, complete cds.
AJ007610 - Homo sapiens mRNA for protocadherin alpha 9 (PCDHA9 gene).
AK314303 - Homo sapiens cDNA, FLJ95060.
BC104802 - Homo sapiens protocadherin alpha 9, mRNA (cDNA clone MGC:132462 IMAGE:8143805), complete cds.
BC104804 - Homo sapiens protocadherin alpha 9, mRNA (cDNA clone MGC:132464 IMAGE:8143807), complete cds.
AB384773 - Synthetic construct DNA, clone: pF1KB3279, Homo sapiens PCDHA9 gene for protocadherin alpha 9 precursor, complete cds, without stop codon, in Flexi system.
KJ892840 - Synthetic construct Homo sapiens clone ccsbBroadEn_02234 PCDHA9 gene, encodes complete protein.
AF152317 - Homo sapiens protocadherin alpha 9 (PCDH-alpha9) mRNA, complete cds.
BC130447 - Homo sapiens protocadherin alpha 10, mRNA (cDNA clone MGC:163319 IMAGE:40146478), complete cds.
HQ258585 - Synthetic construct Homo sapiens clone IMAGE:100073117 protocadherin alpha 10 (PCDHA10), transcript variant 3 (PCDHA10) gene, encodes complete protein.
KJ894313 - Synthetic construct Homo sapiens clone ccsbBroadEn_03707 PCDHA10 gene, encodes complete protein.
AF169689 - Homo sapiens protocadherin alpha 10 alternate isoform (PCDH-alpha10) mRNA, complete cds.
AF152306 - Homo sapiens protocadherin alpha 10 (PCDH-alpha10) mRNA, complete cds.
AJ007609 - Homo sapiens mRNA for protocadherin alpha 11 (PCDHA11 gene).
AB384789 - Synthetic construct DNA, clone: pF1KB3329, Homo sapiens PCDHA11 gene for protocadherin alpha 11 precursor, complete cds, without stop codon, in Flexi system.
AF152307 - Homo sapiens protocadherin alpha 11 (PCDH-alpha11) mRNA, complete cds.
AB384894 - Synthetic construct DNA, clone: pF1KB4085, Homo sapiens PCDHA12 gene for protocadherin alpha 12 precursor, complete cds, without stop codon, in Flexi system.
AF152308 - Homo sapiens protocadherin alpha 12 (PCDH-alpha12) mRNA, complete cds.
AK075556 - Homo sapiens cDNA PSEC0256 fis, clone NT2RP3003549, highly similar to Homo sapiens protocadherin alpha 12 (PCDH-alpha12) mRNA.
AB208924 - Homo sapiens mRNA for protocadherin alpha 13 isoform 1 precursor variant protein.
AF152309 - Homo sapiens protocadherin alpha 13 (PCDH-alpha13) mRNA, complete cds.
AJ007608 - Homo sapiens mRNA for protocadherin alpha-C1 (PCDHAC1 gene).
AF152303 - Homo sapiens protocadherin alpha C1 (PCDH-alpha-C1) mRNA, complete cds.
AK123867 - Homo sapiens cDNA FLJ41873 fis, clone OCBBF2010871, highly similar to Homo sapiens protocadherin alpha C2 (PCDH-alpha-C2) mRNA.
BC063288 - Homo sapiens protocadherin alpha subfamily C, 2, mRNA (cDNA clone MGC:71598 IMAGE:30343089), complete cds.
AF152304 - Homo sapiens protocadherin alpha C2 (PCDH-alpha-C2) mRNA, complete cds.
AF152485 - Homo sapiens protocadherin alpha 7 short form protein (PCDH-alpha7) variable region sequence, complete cds.
JD167065 - Sequence 148089 from Patent EP1572962.
JD132468 - Sequence 113492 from Patent EP1572962.
JD268914 - Sequence 249938 from Patent EP1572962.
JD134550 - Sequence 115574 from Patent EP1572962.
JD134878 - Sequence 115902 from Patent EP1572962.
JD352722 - Sequence 333746 from Patent EP1572962.
JD046762 - Sequence 27786 from Patent EP1572962.
JD428758 - Sequence 409782 from Patent EP1572962.
JD083984 - Sequence 65008 from Patent EP1572962.
JD530511 - Sequence 511535 from Patent EP1572962.
JD314730 - Sequence 295754 from Patent EP1572962.
JD499381 - Sequence 480405 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CNRS4 , NM_018910, O75282, PCDA7_HUMAN, PCDHA7 , Q9UN72, uc324bfv.1
UCSC ID: ENST00000525929.1
RefSeq Accession: NM_018910.3
Protein: Q9UN72 (aka PCDA7_HUMAN or CDA7_HUMAN)

-  Gene Model Information
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-  Methods, Credits, and Use Restrictions
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