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Q9Y5I3 (PCDA1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 125. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Protocadherin alpha-1

Short name=PCDH-alpha-1
Gene names
Name:PCDHA1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length950 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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

Subcellular location

Isoform 1: Cell membrane; Single-pass type I membrane protein By similarity.

Isoform 2: Secreted Potential.

Sequence similarities

Contains 6 cadherin domains.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: Q9Y5I3-1)

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.
Isoform 2 (identifier: Q9Y5I3-2)

The sequence of this isoform differs from the canonical sequence as follows:
     535-798: Missing.
Isoform 3 (identifier: Q9Y5I3-3)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2929 Potential
Chain30 – 950921Protocadherin alpha-1
PRO_0000003884

Regions

Topological domain30 – 697668Extracellular Potential
Transmembrane698 – 71821Helical; Potential
Topological domain719 – 950232Cytoplasmic Potential
Domain30 – 133104Cadherin 1
Domain157 – 24286Cadherin 2
Domain243 – 350108Cadherin 3
Domain351 – 455105Cadherin 4
Domain456 – 565110Cadherin 5
Domain588 – 67891Cadherin 6
Repeat734 – 7374PXXP 1
Repeat799 – 8024PXXP 2
Repeat832 – 8354PXXP 3
Repeat873 – 8764PXXP 4
Repeat891 – 8944PXXP 5
Region734 – 8941615 X 4 AA repeats of P-X-X-P
Compositional bias923 – 9308Poly-Lys

Amino acid modifications

Glycosylation2571N-linked (GlcNAc...) Potential
Glycosylation2651N-linked (GlcNAc...) Potential
Glycosylation5481N-linked (GlcNAc...) Potential

Natural variations

Alternative sequence535 – 798264Missing in isoform 2.
VSP_000670
Alternative sequence799 – 8079PRQPNPDWR → VSPTFEFWL in isoform 3.
VSP_000671
Alternative sequence808 – 950143Missing in isoform 3.
VSP_000672
Natural variant3601R → G.
Corresponds to variant rs34575154 [ dbSNP | Ensembl ].
VAR_048521
Natural variant4491N → H.
Corresponds to variant rs3733712 [ dbSNP | Ensembl ].
VAR_021872
Natural variant7321Y → C.
Corresponds to variant rs2240696 [ dbSNP | Ensembl ].
VAR_021873
Natural variant7591C → F.
Corresponds to variant rs2240695 [ dbSNP | Ensembl ].
VAR_048522

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 1, 1999. Version 1.
Checksum: 9FC170365565908A

FASTA950102,952
        10         20         30         40         50         60 
MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ DLGLELAELV 

        70         80         90        100        110        120 
PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA ECSIHLELIA DRPLQVFHVE 

       130        140        150        160        170        180 
VKVKDINDNP PVFRGREQII FIPESRLLNS RFPIEGAADA DIGANALLTY TLSPSDYFSL 

       190        200        210        220        230        240 
DVEASDELSK SLWLELRKYL DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP 

       250        260        270        280        290        300 
LFDQAVYRVH LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG 

       310        320        330        340        350        360 
EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL AVTSLYLPIR 

       370        380        390        400        410        420 
EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST FKNYYSLVLD SALDRESLSV 

       430        440        450        460        470        480 
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR 

       490        500        510        520        530        540 
DADAQENALV SYSLVERRVG ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA 

       550        560        570        580        590        600 
GVPPLGSNVT LQVFVLDEND NAPALLAPRV GGTIGAVSEL VPRLVGAGHV VAKVRAVDAD 

       610        620        630        640        650        660 
SGYNAWLSYE LQPAAGGARI PFRVGLYTGE ISTTRVLDEA DLSRYRLLVL VKDHGEPALT 

       670        680        690        700        710        720 
ATATVLVSLV ESGQAPKASS RASVGVAGPE AALVDVNVYL IIAICAVSSL LVLTLLLYTA 

       730        740        750        760        770        780 
LRCSVPPTEG AYVPGKPTLV CSSALGSWSN SQQRRQRVCS SEGPPKTDLM AFSPGLSPSL 

       790        800        810        820        830        840 
NTSERNEQPE ANLDLSGNPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP 

       850        860        870        880        890        900 
TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR 

       910        920        930        940        950 
QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ 

« Hide

Isoform 2 [UniParc].

Checksum: 07938F6D1B0154CC
Show »

FASTA68675,542
Isoform 3 [UniParc].

Checksum: 93A98867A6AE6D7D
Show »

FASTA80787,639

References

« Hide 'large scale' references
[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. expand/collapse author list , 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].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF152305 mRNA. Translation: AAD43699.1.
AF152479 mRNA. Translation: AAD43740.1.
AF169695 mRNA. Translation: AAF89692.1.
AC005609 Genomic DNA. Translation: AAC34325.1.
CCDSCCDS54912.1. [Q9Y5I3-2]
CCDS54913.1. [Q9Y5I3-1]
RefSeqNP_061723.1. NM_018900.3. [Q9Y5I3-1]
NP_113598.1. NM_031410.2. [Q9Y5I3-3]
NP_113599.1. NM_031411.2. [Q9Y5I3-2]
UniGeneHs.199343.

3D structure databases

ProteinModelPortalQ9Y5I3.
SMRQ9Y5I3. Positions 27-667.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ9Y5I3. 1 interaction.
STRING9606.ENSP00000367373.

PTM databases

PhosphoSiteQ9Y5I3.

Polymorphism databases

DMDM13878434.

Proteomic databases

PaxDbQ9Y5I3.
PRIDEQ9Y5I3.

Protocols and materials databases

DNASU56147.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000378133; ENSP00000367373; ENSG00000204970. [Q9Y5I3-3]
ENST00000394633; ENSP00000378129; ENSG00000204970. [Q9Y5I3-2]
ENST00000504120; ENSP00000420840; ENSG00000204970. [Q9Y5I3-1]
ENST00000608256; ENSP00000477468; ENSG00000273078. [Q9Y5I3-1]
ENST00000608508; ENSP00000476685; ENSG00000273078. [Q9Y5I3-2]
ENST00000610163; ENSP00000476445; ENSG00000273078. [Q9Y5I3-3]
GeneID56147.
KEGGhsa:56147.
UCSCuc003lgz.3. human. [Q9Y5I3-3]
uc003lha.2. human. [Q9Y5I3-2]
uc003lhb.2. human. [Q9Y5I3-1]

Organism-specific databases

CTD56147.
GeneCardsGC05P140146.
GC05P140147.
H-InvDBHIX0032383.
HGNCHGNC:8663. PCDHA1.
HPAHPA008712.
HPA035969.
MIM604966. gene.
606307. gene.
neXtProtNX_Q9Y5I3.
PharmGKBPA33009.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG267459.
HOGENOMHOG000220892.
HOVERGENHBG054878.
InParanoidQ9Y5I3.
KOK16493.
OMANEQPEAN.
OrthoDBEOG7KSX80.
PhylomeDBQ9Y5I3.
TreeFamTF332299.

Gene expression databases

BgeeQ9Y5I3.
GenevestigatorQ9Y5I3.

Family and domain databases

Gene3D2.60.40.60. 6 hits.
InterProIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
[Graphical view]
PRINTSPR00205. CADHERIN.
SMARTSM00112. CA. 6 hits.
[Graphical view]
SUPFAMSSF49313. SSF49313. 6 hits.
PROSITEPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSPCDHA1. human.
GeneWikiProtocadherin_alpha_1.
GenomeRNAi56147.
NextBio61750.
PROQ9Y5I3.
SOURCESearch...

Entry information

Entry namePCDA1_HUMAN
AccessionPrimary (citable) accession number: Q9Y5I3
Secondary accession number(s): O75288, Q9NRT7
Entry history
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 1, 1999
Last modified: July 9, 2014
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 5

Human chromosome 5: entries, gene names and cross-references to MIM