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Protein

Protocadherin alpha-1

Gene

PCDHA1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

  • cell adhesion Source: ProtInc
  • cell-cell signaling Source: GO_Central
  • homophilic cell adhesion via plasma membrane adhesion molecules Source: InterPro
  • nervous system development Source: ProtInc

Keywordsi

Biological processCell adhesion
LigandCalcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin alpha-1
Short name:
PCDH-alpha-1
Gene namesi
Name:PCDHA1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

EuPathDBiHostDB:ENSG00000204970.9
HGNCiHGNC:8663 PCDHA1
MIMi604966 gene
606307 gene
neXtProtiNX_Q9Y5I3

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini30 – 697ExtracellularSequence analysisAdd BLAST668
Transmembranei698 – 718HelicalSequence analysisAdd BLAST21
Topological domaini719 – 950CytoplasmicSequence analysisAdd BLAST232

Keywords - Cellular componenti

Cell membrane, Membrane, Secreted

Pathology & Biotechi

Organism-specific databases

DisGeNETi56147
OpenTargetsiENSG00000204970
PharmGKBiPA33009

Polymorphism and mutation databases

BioMutaiPCDHA1
DMDMi13878434

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 29Sequence analysisAdd BLAST29
ChainiPRO_000000388430 – 950Protocadherin alpha-1Add BLAST921

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi257N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi265N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi548N-linked (GlcNAc...) asparagineSequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ9Y5I3
PaxDbiQ9Y5I3
PeptideAtlasiQ9Y5I3
PRIDEiQ9Y5I3
ProteomicsDBi86411
86412 [Q9Y5I3-2]
86413 [Q9Y5I3-3]

PTM databases

iPTMnetiQ9Y5I3
PhosphoSitePlusiQ9Y5I3

Expressioni

Gene expression databases

BgeeiENSG00000204970
GenevisibleiQ9Y5I3 HS

Organism-specific databases

HPAiHPA035969

Interactioni

Protein-protein interaction databases

BioGridi121087, 4 interactors
IntActiQ9Y5I3, 1 interactor
STRINGi9606.ENSP00000420840

Structurei

3D structure databases

ProteinModelPortaliQ9Y5I3
SMRiQ9Y5I3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini30 – 133Cadherin 1PROSITE-ProRule annotationAdd BLAST104
Domaini157 – 242Cadherin 2PROSITE-ProRule annotationAdd BLAST86
Domaini243 – 350Cadherin 3PROSITE-ProRule annotationAdd BLAST108
Domaini351 – 455Cadherin 4PROSITE-ProRule annotationAdd BLAST105
Domaini456 – 565Cadherin 5PROSITE-ProRule annotationAdd BLAST110
Domaini588 – 678Cadherin 6PROSITE-ProRule annotationAdd BLAST91
Repeati734 – 737PXXP 14
Repeati799 – 802PXXP 24
Repeati832 – 835PXXP 34
Repeati873 – 876PXXP 44
Repeati891 – 894PXXP 54

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni734 – 8945 X 4 AA repeats of P-X-X-PAdd BLAST161

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi923 – 930Poly-Lys8

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3594 Eukaryota
ENOG410XQHI LUCA
GeneTreeiENSGT00920000148958
HOGENOMiHOG000220892
HOVERGENiHBG054878
InParanoidiQ9Y5I3
KOiK16493
OMAiNEQPEAN
OrthoDBiEOG091G00KR
PhylomeDBiQ9Y5I3
TreeFamiTF332299

Family and domain databases

InterProiView protein in InterPro
IPR002126 Cadherin
IPR015919 Cadherin-like
IPR031904 Cadherin_CBD
IPR020894 Cadherin_CS
IPR013164 Cadherin_N
IPR030740 PCDHA1
PANTHERiPTHR24028:SF92 PTHR24028:SF92, 1 hit
PfamiView protein in Pfam
PF00028 Cadherin, 5 hits
PF08266 Cadherin_2, 1 hit
PF15974 Cadherin_tail, 1 hit
PRINTSiPR00205 CADHERIN
SMARTiView protein in SMART
SM00112 CA, 6 hits
SUPFAMiSSF49313 SSF49313, 6 hits
PROSITEiView protein in PROSITE
PS00232 CADHERIN_1, 5 hits
PS50268 CADHERIN_2, 6 hits

Sequences (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: Q9Y5I3-1) [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
MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ
60 70 80 90 100
DLGLELAELV PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA
110 120 130 140 150
ECSIHLELIA DRPLQVFHVE VKVKDINDNP PVFRGREQII FIPESRLLNS
160 170 180 190 200
RFPIEGAADA DIGANALLTY TLSPSDYFSL DVEASDELSK SLWLELRKYL
210 220 230 240 250
DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP LFDQAVYRVH
260 270 280 290 300
LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG
310 320 330 340 350
EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL
360 370 380 390 400
AVTSLYLPIR EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST
410 420 430 440 450
FKNYYSLVLD SALDRESLSV YELVVTARDG GSPSLWATAR VSVEVADVND
460 470 480 490 500
NAPAFAQPEY TVFVKENNPP GCHIFTVSAR DADAQENALV SYSLVERRVG
510 520 530 540 550
ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA GVPPLGSNVT
560 570 580 590 600
LQVFVLDEND NAPALLAPRV GGTIGAVSEL VPRLVGAGHV VAKVRAVDAD
610 620 630 640 650
SGYNAWLSYE LQPAAGGARI PFRVGLYTGE ISTTRVLDEA DLSRYRLLVL
660 670 680 690 700
VKDHGEPALT ATATVLVSLV ESGQAPKASS RASVGVAGPE AALVDVNVYL
710 720 730 740 750
IIAICAVSSL LVLTLLLYTA LRCSVPPTEG AYVPGKPTLV CSSALGSWSN
760 770 780 790 800
SQQRRQRVCS SEGPPKTDLM AFSPGLSPSL NTSERNEQPE ANLDLSGNPR
810 820 830 840 850
QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP TVSSATPEPE
860 870 880 890 900
AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
910 920 930 940 950
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ
Length:950
Mass (Da):102,952
Last modified:November 1, 1999 - v1
Checksum:i9FC170365565908A
GO
Isoform 2 (identifier: Q9Y5I3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     535-798: Missing.

Show »
Length:686
Mass (Da):75,542
Checksum:i07938F6D1B0154CC
GO
Isoform 3 (identifier: Q9Y5I3-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     799-807: PRQPNPDWR → VSPTFEFWL
     808-950: Missing.

Show »
Length:807
Mass (Da):87,639
Checksum:i93A98867A6AE6D7D
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_048521360R → G. Corresponds to variant dbSNP:rs34575154Ensembl.1
Natural variantiVAR_021872449N → H. Corresponds to variant dbSNP:rs3733712Ensembl.1
Natural variantiVAR_021873732Y → C. Corresponds to variant dbSNP:rs2240696Ensembl.1
Natural variantiVAR_048522759C → F. Corresponds to variant dbSNP:rs2240695Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_000670535 – 798Missing in isoform 2. CuratedAdd BLAST264
Alternative sequenceiVSP_000671799 – 807PRQPNPDWR → VSPTFEFWL in isoform 3. 1 Publication9
Alternative sequenceiVSP_000672808 – 950Missing in isoform 3. 1 PublicationAdd BLAST143

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152305 mRNA Translation: AAD43699.1
AF152479 mRNA Translation: AAD43740.1
AF169695 mRNA Translation: AAF89692.1
AC005609 Genomic DNA Translation: AAC34325.1
CCDSiCCDS54912.1 [Q9Y5I3-2]
CCDS54913.1 [Q9Y5I3-1]
RefSeqiNP_061723.1, NM_018900.3 [Q9Y5I3-1]
NP_113598.1, NM_031410.2 [Q9Y5I3-3]
NP_113599.1, NM_031411.2 [Q9Y5I3-2]
UniGeneiHs.199343

Genome annotation databases

EnsembliENST00000378133; ENSP00000367373; ENSG00000204970 [Q9Y5I3-3]
ENST00000394633; ENSP00000378129; ENSG00000204970 [Q9Y5I3-2]
ENST00000504120; ENSP00000420840; ENSG00000204970 [Q9Y5I3-1]
GeneIDi56147
KEGGihsa:56147
UCSCiuc003lgz.5 human [Q9Y5I3-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiPCDA1_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5I3
Secondary accession number(s): O75288, Q9NRT7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 1, 1999
Last modified: June 20, 2018
This is version 158 of the entry and version 1 of the sequence. See 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

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