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Protein

Protocadherin alpha-4

Gene

PCDHA4

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

  1. calcium ion binding Source: InterPro

GO - Biological processi

  1. cell adhesion Source: ProtInc
  2. homophilic cell adhesion via plasma membrane adhesion molecules Source: InterPro
  3. nervous system development Source: ProtInc
Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin alpha-4
Short name:
PCDH-alpha-4
Gene namesi
Name:PCDHA4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8670. PCDHA4.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini30 – 697668ExtracellularSequence AnalysisAdd
BLAST
Transmembranei698 – 71821HelicalSequence AnalysisAdd
BLAST
Topological domaini719 – 947229CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. integral component of plasma membrane Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33016.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2929Sequence AnalysisAdd
BLAST
Chaini30 – 947918Protocadherin alpha-4PRO_0000003890Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi139 – 1391N-linked (GlcNAc...)Sequence Analysis
Glycosylationi257 – 2571N-linked (GlcNAc...)Sequence Analysis
Glycosylationi265 – 2651N-linked (GlcNAc...)Sequence Analysis
Glycosylationi548 – 5481N-linked (GlcNAc...)Sequence Analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ9UN74.
PRIDEiQ9UN74.

PTM databases

PhosphoSiteiQ9UN74.

Expressioni

Gene expression databases

BgeeiQ9UN74.
ExpressionAtlasiQ9UN74. baseline.
GenevestigatoriQ9UN74.

Organism-specific databases

HPAiHPA043180.

Interactioni

Subunit structurei

Interacts with FYN.By similarity

Protein-protein interaction databases

BioGridi121084. 14 interactions.
IntActiQ9UN74. 13 interactions.
MINTiMINT-1368168.
STRINGi9606.ENSP00000349344.

Structurei

3D structure databases

ProteinModelPortaliQ9UN74.
SMRiQ9UN74. Positions 27-683.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini30 – 133104Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini134 – 242109Cadherin 2PROSITE-ProRule annotationAdd
BLAST
Domaini243 – 350108Cadherin 3PROSITE-ProRule annotationAdd
BLAST
Domaini351 – 455105Cadherin 4PROSITE-ProRule annotationAdd
BLAST
Domaini456 – 565110Cadherin 5PROSITE-ProRule annotationAdd
BLAST
Domaini588 – 67891Cadherin 6PROSITE-ProRule annotationAdd
BLAST
Repeati734 – 7374PXXP 1
Repeati774 – 7774PXXP 2
Repeati796 – 7994PXXP 3
Repeati829 – 8324PXXP 4
Repeati870 – 8734PXXP 5
Repeati888 – 8914PXXP 6

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni734 – 8911586 X 4 AA repeats of P-X-X-PAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi920 – 9278Poly-Lys

Sequence similaritiesi

Contains 6 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG267459.
GeneTreeiENSGT00780000121859.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9UN74.
KOiK16493.
OMAiDNVPDLE.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9UN74.
TreeFamiTF332299.

Family and domain databases

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

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9UN74-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MEFSWGSGQE SRRLLLLLLL LAAWEAGNGQ LHYSVSEEAK HGTFVGRIAQ
60 70 80 90 100
DLGLELAELV PRLFRVASKG RGGLLEVNLQ NGILFVNSRI DREELCRRSA
110 120 130 140 150
ECSIHLEVIV DRPLQVFHVD VEVRDINDNP PVFPATQKNL SIAESRPLDS
160 170 180 190 200
RFPLEGASDA DIGENALLTY RLSPNEYFSL EKPPDDELVK GLGLILRKSL
210 220 230 240 250
DREEAPEIFL VLTATDGGKP ELTGTVQLLI TVLDANDNAP AFDRTIYKVR
260 270 280 290 300
LLENVPNGTL VIKLNASDLD EGLNGDIVYS FSNDISPNVK SKFHIDPITG
310 320 330 340 350
QIIVKGYIDF EESKSYEIIV EGIDKGQLPL SGHCRVIVEV EDNNDNVPDL
360 370 380 390 400
EFKSLSLPIR EDAPLGTVIA LISVSDKDMG VNGLVTCSLT SHVPFKLVST
410 420 430 440 450
FKNYYSLVLD SALDRESVSA YELVVTARDG GSPSLWATAS VSVEVADVND
460 470 480 490 500
NAPAFAQPEY TVFVKENNPP GCHIFTVSAW DADAQENALV SYSLVERRVG
510 520 530 540 550
ERALSSYVSV HAESGKVYAL QPLDHEELEL LQFQVTARDA GVPPLGSNVT
560 570 580 590 600
LQVFVLDEND NAPALLAPRA GGTGGAVSEL VPWSVGVGHV VAKVRAVDAD
610 620 630 640 650
SGYNAWLSYE LQPGTGGARI PFRVGLYTGE ISTTRALDET DAPRHRLLVL
660 670 680 690 700
VKDHGEPALT ATATVLVSLV ESGQAPKASS RALVGAVGPD AALVDVNVYL
710 720 730 740 750
IIAICAVSSL LVLTLLLYTA LRCSALPTEG ACAPGKPTLV CSSAVGSWSY
760 770 780 790 800
SQQRRPRVCS GEGPPKTDLM AFSPSLPDSR DREDQLQTTE ESFAKPRQPN
810 820 830 840 850
PDWRYSASLR AGMHSSVHLE EAGILRAGPG GPDQQWPTVS SATPEPEAGE
860 870 880 890 900
VSPPVGAGVN SNSWTFKYGP GNPKQSGPGE LPDKFIIPGS PAIISIRQEP
910 920 930 940
TNSQIDKSDF ITFGKKEETK KKKKKKKGNK TQEKKEKGNS TTDNSDQ
Length:947
Mass (Da):102,293
Last modified:April 30, 2000 - v1
Checksum:i2B06F20872D731D8
GO
Isoform 2 (identifier: Q9UN74-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     796-798: PRQ → VSV
     799-947: Missing.

Show »
Length:798
Mass (Da):86,158
Checksum:i9EF890C30F48A77F
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti55 – 551E → D.
Corresponds to variant rs11167605 [ dbSNP | Ensembl ].
VAR_059180
Natural varianti184 – 1841P → S.
Corresponds to variant rs3822346 [ dbSNP | Ensembl ].
VAR_024390

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei796 – 7983PRQ → VSV in isoform 2. 2 PublicationsVSP_000677
Alternative sequencei799 – 947149Missing in isoform 2. 2 PublicationsVSP_000678Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152312 mRNA. Translation: AAD43706.1.
AF152482 mRNA. Translation: AAD43743.1.
AC005609 Genomic DNA. Translation: AAC34322.1.
BC112102 mRNA. Translation: AAI12103.1.
BC113609 mRNA. Translation: AAI13610.1.
CCDSiCCDS54916.1. [Q9UN74-1]
RefSeqiNP_061730.1. NM_018907.3. [Q9UN74-1]
NP_113688.1. NM_031500.2. [Q9UN74-2]
UniGeneiHs.199343.

Genome annotation databases

EnsembliENST00000530339; ENSP00000435300; ENSG00000204967. [Q9UN74-1]
ENST00000618834; ENSP00000481220; ENSG00000204967. [Q9UN74-2]
GeneIDi56144.
KEGGihsa:56144.
UCSCiuc003lhi.2. human. [Q9UN74-1]
uc011daa.2. human. [Q9UN74-2]

Polymorphism databases

DMDMi13878424.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152312 mRNA. Translation: AAD43706.1.
AF152482 mRNA. Translation: AAD43743.1.
AC005609 Genomic DNA. Translation: AAC34322.1.
BC112102 mRNA. Translation: AAI12103.1.
BC113609 mRNA. Translation: AAI13610.1.
CCDSiCCDS54916.1. [Q9UN74-1]
RefSeqiNP_061730.1. NM_018907.3. [Q9UN74-1]
NP_113688.1. NM_031500.2. [Q9UN74-2]
UniGeneiHs.199343.

3D structure databases

ProteinModelPortaliQ9UN74.
SMRiQ9UN74. Positions 27-683.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121084. 14 interactions.
IntActiQ9UN74. 13 interactions.
MINTiMINT-1368168.
STRINGi9606.ENSP00000349344.

PTM databases

PhosphoSiteiQ9UN74.

Polymorphism databases

DMDMi13878424.

Proteomic databases

PaxDbiQ9UN74.
PRIDEiQ9UN74.

Protocols and materials databases

DNASUi56144.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000530339; ENSP00000435300; ENSG00000204967. [Q9UN74-1]
ENST00000618834; ENSP00000481220; ENSG00000204967. [Q9UN74-2]
GeneIDi56144.
KEGGihsa:56144.
UCSCiuc003lhi.2. human. [Q9UN74-1]
uc011daa.2. human. [Q9UN74-2]

Organism-specific databases

CTDi56144.
GeneCardsiGC05P140186.
HGNCiHGNC:8670. PCDHA4.
HPAiHPA043180.
MIMi604966. gene.
606310. gene.
neXtProtiNX_Q9UN74.
PharmGKBiPA33016.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG267459.
GeneTreeiENSGT00780000121859.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9UN74.
KOiK16493.
OMAiDNVPDLE.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9UN74.
TreeFamiTF332299.

Miscellaneous databases

GeneWikiiPCDHA4.
GenomeRNAii56144.
NextBioi61732.
PROiQ9UN74.
SOURCEiSearch...

Gene expression databases

BgeeiQ9UN74.
ExpressionAtlasiQ9UN74. baseline.
GenevestigatoriQ9UN74.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 6 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(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
    Tissue: Brain.
  2. "The DNA sequence and comparative analysis of human chromosome 5."
    Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.
    , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
    Nature 431:268-274(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Lung.

Entry informationi

Entry nameiPCDA4_HUMAN
AccessioniPrimary (citable) accession number: Q9UN74
Secondary accession number(s): O75285, Q2M253
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2001
Last sequence update: April 30, 2000
Last modified: March 3, 2015
This is version 127 of the entry and version 1 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

External Data

Dasty 3

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 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.