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Protein

Protocadherin alpha-1

Gene

PCDHA1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 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-1
Short name:
PCDH-alpha-1
Gene namesi
Name:PCDHA1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 5

Organism-specific databases

HGNCiHGNC:8663. PCDHA1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini30 – 697668ExtracellularSequence AnalysisAdd
BLAST
Transmembranei698 – 71821HelicalSequence AnalysisAdd
BLAST
Topological domaini719 – 950232CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. extracellular region Source: UniProtKB-SubCell
  2. integral component of plasma membrane Source: ProtInc
  3. plasma membrane Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane, Secreted

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33009.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2929Sequence AnalysisAdd
BLAST
Chaini30 – 950921Protocadherin alpha-1PRO_0000003884Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ9Y5I3.
PRIDEiQ9Y5I3.

PTM databases

PhosphoSiteiQ9Y5I3.

Expressioni

Gene expression databases

BgeeiQ9Y5I3.
GenevestigatoriQ9Y5I3.

Organism-specific databases

HPAiHPA035969.

Interactioni

Protein-protein interaction databases

IntActiQ9Y5I3. 1 interaction.
STRINGi9606.ENSP00000367373.

Structurei

3D structure databases

ProteinModelPortaliQ9Y5I3.
SMRiQ9Y5I3. Positions 27-667.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini30 – 133104Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini157 – 24286Cadherin 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
Repeati799 – 8024PXXP 2
Repeati832 – 8354PXXP 3
Repeati873 – 8764PXXP 4
Repeati891 – 8944PXXP 5

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni734 – 8941615 X 4 AA repeats of P-X-X-PAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi923 – 9308Poly-Lys

Sequence similaritiesi

Contains 6 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG267459.
GeneTreeiENSGT00780000121859.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5I3.
KOiK16493.
OMAiNEQPEAN.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9Y5I3.
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 (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)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti360 – 3601R → G.
Corresponds to variant rs34575154 [ dbSNP | Ensembl ].
VAR_048521
Natural varianti449 – 4491N → H.
Corresponds to variant rs3733712 [ dbSNP | Ensembl ].
VAR_021872
Natural varianti732 – 7321Y → C.
Corresponds to variant rs2240696 [ dbSNP | Ensembl ].
VAR_021873
Natural varianti759 – 7591C → F.
Corresponds to variant rs2240695 [ dbSNP | Ensembl ].
VAR_048522

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei535 – 798264Missing in isoform 2. CuratedVSP_000670Add
BLAST
Alternative sequencei799 – 8079PRQPNPDWR → VSPTFEFWL in isoform 3. 1 PublicationVSP_000671
Alternative sequencei808 – 950143Missing in isoform 3. 1 PublicationVSP_000672Add
BLAST

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.3. human. [Q9Y5I3-3]
uc003lha.2. human. [Q9Y5I3-2]
uc003lhb.2. human. [Q9Y5I3-1]

Polymorphism databases

DMDMi13878434.

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliQ9Y5I3.
SMRiQ9Y5I3. Positions 27-667.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ9Y5I3. 1 interaction.
STRINGi9606.ENSP00000367373.

PTM databases

PhosphoSiteiQ9Y5I3.

Polymorphism databases

DMDMi13878434.

Proteomic databases

PaxDbiQ9Y5I3.
PRIDEiQ9Y5I3.

Protocols and materials databases

DNASUi56147.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000378133; ENSP00000367373; ENSG00000204970. [Q9Y5I3-3]
ENST00000394633; ENSP00000378129; ENSG00000204970. [Q9Y5I3-2]
ENST00000504120; ENSP00000420840; ENSG00000204970. [Q9Y5I3-1]
GeneIDi56147.
KEGGihsa:56147.
UCSCiuc003lgz.3. human. [Q9Y5I3-3]
uc003lha.2. human. [Q9Y5I3-2]
uc003lhb.2. human. [Q9Y5I3-1]

Organism-specific databases

CTDi56147.
GeneCardsiGC05P140146.
GC05P140147.
H-InvDBHIX0032383.
HGNCiHGNC:8663. PCDHA1.
HPAiHPA035969.
MIMi604966. gene.
606307. gene.
neXtProtiNX_Q9Y5I3.
PharmGKBiPA33009.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG267459.
GeneTreeiENSGT00780000121859.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5I3.
KOiK16493.
OMAiNEQPEAN.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9Y5I3.
TreeFamiTF332299.

Miscellaneous databases

ChiTaRSiPCDHA1. human.
GeneWikiiProtocadherin_alpha_1.
GenomeRNAii56147.
NextBioi61750.
PROiQ9Y5I3.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y5I3.
GenevestigatoriQ9Y5I3.

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(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 3).
    Tissue: Brain.
  2. "Alternative splicing within the human CNR family of protocadherins (PCDH-alpha) produces transcripts encoding secreted proteins."
    Kools P.F.J., van Roy F.
    Submitted (JUL-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE (ISOFORM 2).
    Tissue: Brain.
  3. "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(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiPCDA1_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5I3
Secondary accession number(s): O75288, Q9NRT7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 1, 1999
Last modified: March 4, 2015
This is version 131 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.