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Protein

Protocadherin beta-9

Gene

PCDHB9

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

GO - Molecular functioni

GO - Biological processi

  • calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules Source: UniProtKB
  • homophilic cell adhesion via plasma membrane adhesion molecules Source: InterPro
  • synapse assembly Source: UniProtKB
  • synaptic transmission Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin beta-9
Short name:
PCDH-beta-9
Alternative name(s):
Protocadherin-3H
Gene namesi
Name:PCDHB9
Synonyms:PCDH3H
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8694. PCDHB9.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini27 – 690664ExtracellularSequence analysisAdd
BLAST
Transmembranei691 – 71121HelicalSequence analysisAdd
BLAST
Topological domaini712 – 79786CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • integral component of membrane Source: UniProtKB
  • plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33043.

Polymorphism and mutation databases

DMDMi13431372.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2626Sequence analysisAdd
BLAST
Chaini27 – 797771Protocadherin beta-9PRO_0000003930Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi169 – 1691N-linked (GlcNAc...)Sequence analysis
Glycosylationi418 – 4181N-linked (GlcNAc...)Sequence analysis
Glycosylationi567 – 5671N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ9Y5E1.
PeptideAtlasiQ9Y5E1.
PRIDEiQ9Y5E1.

PTM databases

iPTMnetiQ9Y5E1.

Expressioni

Gene expression databases

CleanExiHS_PCDHB9.
ExpressionAtlasiQ9Y5E1. baseline and differential.
GenevisibleiQ9Y5E1. HS.

Organism-specific databases

HPAiHPA013445.
HPA029441.

Structurei

3D structure databases

ProteinModelPortaliQ9Y5E1.
SMRiQ9Y5E1. Positions 33-677.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini35 – 13399Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini138 – 242105Cadherin 2PROSITE-ProRule annotationAdd
BLAST
Domaini247 – 347101Cadherin 3PROSITE-ProRule annotationAdd
BLAST
Domaini352 – 451100Cadherin 4PROSITE-ProRule annotationAdd
BLAST
Domaini456 – 561106Cadherin 5PROSITE-ProRule annotationAdd
BLAST
Domaini568 – 671104Cadherin 6PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 6 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

HOVERGENiHBG054878.
InParanoidiQ9Y5E1.
KOiK16494.

Family and domain databases

Gene3Di2.60.40.60. 5 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_2. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 5 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 6 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9Y5E1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTRGFSFPR QRQVLFLFLF WGVSLAGSGF GRYSVTEETE KGSFVVNLAK
60 70 80 90 100
DLGLAEGELA ARGTRVVSDD NKQYLLLDSH TGNLLTNEKL DREKLCGPKE
110 120 130 140 150
PCMLYFQILM DDPFQIYRAE LRVRDINDHS PVFRHKEMVL KISENTAEGT
160 170 180 190 200
AFRLERAQDP DEGHNSIQNY TISSNSFFHI KISGSDEGMI YPELVLDKAL
210 220 230 240 250
DREEQEELSL TLTALDGGSP SRSGTSTIRI VVLDVNDNAP QFAQALYETQ
260 270 280 290 300
APENSPVGSL IVKVSAGDAD SGVNAEVSYS FFDASEDILT TFQINPFSGE
310 320 330 340 350
IFLRELLDYE LVNSYKINIQ AMDGGGLSAR CTVLIKVLDS NDNPPELIIS
360 370 380 390 400
SLSNSVAENS PGIVLAVFKI KDRDSGENGK TICYVQDNLP FFLKPSVDNF
410 420 430 440 450
YILMTEGALD RESKAEYNIT ITVTDLGTPR LKTEHSITLQ VSDVNDNAPA
460 470 480 490 500
FTQTSYTLFV RENNSPALHI GSVSATDRDS GTNAQVTYSL LPPQDPHLPL
510 520 530 540 550
ASLVSINADN GHLFALRSLD YEALQAFDFR VGASDRGSPA LSSEALVRVL
560 570 580 590 600
VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
610 620 630 640 650
WLSYQLLKAT EPGLFGVWAH NGEVRTARLL SERDAAKHRL VVLVKDNGEP
660 670 680 690 700
PRSATATLHV LLVDGFSQPY LPLPEAAPAQ AQADLLTVYL VVALASVSSL
710 720 730 740 750
FLLSVLLFVA VRLCRRSRAA SVGRCSVPEG PFPGHLVDVS GTGTLFQSYQ
760 770 780 790
YEVCLTGGSE TGEFKFLKPI TPHLPPHRGG KEIEENSTLP NSFGFNY
Length:797
Mass (Da):87,099
Last modified:March 1, 2001 - v2
Checksum:i53E9D944BA903062
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti124 – 1241R → S.2 Publications
Corresponds to variant rs2740588 [ dbSNP | Ensembl ].
VAR_061064
Natural varianti174 – 1741S → P.
Corresponds to variant rs11167742 [ dbSNP | Ensembl ].
VAR_059186
Natural varianti185 – 1851S → G.
Corresponds to variant rs17844512 [ dbSNP | Ensembl ].
VAR_061065
Natural varianti239 – 2391A → V.1 Publication
Corresponds to variant rs11167743 [ dbSNP | Ensembl ].
VAR_059187
Natural varianti414 – 4141K → E.
Corresponds to variant rs10040383 [ dbSNP | Ensembl ].
VAR_061066
Natural varianti426 – 4261L → M.2 Publications
Corresponds to variant rs2697530 [ dbSNP | Ensembl ].
VAR_061067

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152502 mRNA. Translation: AAD43763.2.
AF217749 mRNA. Translation: AAF81913.1.
BC100672 mRNA. Translation: AAI00673.1.
BC105636 mRNA. Translation: AAI05637.1.
BC105640 mRNA. Translation: AAI05641.1.
AF282973 Genomic DNA. Translation: AAG10032.1.
CCDSiCCDS75328.1.
RefSeqiNP_061992.3. NM_019119.4.
UniGeneiHs.662726.

Genome annotation databases

EnsembliENST00000316105; ENSP00000478606; ENSG00000177839.
GeneIDi56127.
KEGGihsa:56127.
UCSCiuc032vnm.2. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152502 mRNA. Translation: AAD43763.2.
AF217749 mRNA. Translation: AAF81913.1.
BC100672 mRNA. Translation: AAI00673.1.
BC105636 mRNA. Translation: AAI05637.1.
BC105640 mRNA. Translation: AAI05641.1.
AF282973 Genomic DNA. Translation: AAG10032.1.
CCDSiCCDS75328.1.
RefSeqiNP_061992.3. NM_019119.4.
UniGeneiHs.662726.

3D structure databases

ProteinModelPortaliQ9Y5E1.
SMRiQ9Y5E1. Positions 33-677.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

iPTMnetiQ9Y5E1.

Polymorphism and mutation databases

DMDMi13431372.

Proteomic databases

EPDiQ9Y5E1.
PeptideAtlasiQ9Y5E1.
PRIDEiQ9Y5E1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000316105; ENSP00000478606; ENSG00000177839.
GeneIDi56127.
KEGGihsa:56127.
UCSCiuc032vnm.2. human.

Organism-specific databases

CTDi56127.
GeneCardsiPCDHB9.
HGNCiHGNC:8694. PCDHB9.
HPAiHPA013445.
HPA029441.
MIMi604967. gene.
606335. gene.
neXtProtiNX_Q9Y5E1.
PharmGKBiPA33043.
GenAtlasiSearch...

Phylogenomic databases

HOVERGENiHBG054878.
InParanoidiQ9Y5E1.
KOiK16494.

Miscellaneous databases

GeneWikiiPCDHB9.
GenomeRNAii56127.
PROiQ9Y5E1.
SOURCEiSearch...

Gene expression databases

CleanExiHS_PCDHB9.
ExpressionAtlasiQ9Y5E1. baseline and differential.
GenevisibleiQ9Y5E1. HS.

Family and domain databases

Gene3Di2.60.40.60. 5 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_2. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 5 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 6 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A striking organization of a large family of human neural cadherin-like cell adhesion genes."
    Wu Q., Maniatis T.
    Cell 97:779-790(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. Wu Q., Maniatis T.
    Submitted (NOV-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION.
  3. "The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number."
    Vanhalst K., Kools P., Vanden Eynde E., van Roy F.
    FEBS Lett. 495:120-125(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANTS SER-124 AND MET-426.
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT VAL-239.
  5. "Molecular analysis of the human protocadherin-3 (PCDH-beta) gene cluster."
    Kools P.F.J., van Roy F.
    Submitted (JUN-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-536, VARIANTS SER-124 AND MET-426.

Entry informationi

Entry nameiPCDB9_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5E1
Secondary accession number(s): Q2M2U8, Q496X9, Q9NRJ8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: March 1, 2001
Last modified: July 6, 2016
This is version 124 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.