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Q9Y5I3

- PCDA1_HUMAN

UniProt

Q9Y5I3 - PCDA1_HUMAN

Protein

Protocadherin alpha-1

Gene

PCDHA1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 126 (01 Oct 2014)
      Sequence version 1 (01 Nov 1999)
      Previous versions | rss
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    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 Source: InterPro
    3. nervous system development Source: ProtInc

    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

    GO - Cellular componenti

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

    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

    HPAiHPA008712.
    HPA035969.

    Interactioni

    Protein-protein interaction databases

    IntActiQ9Y5I3. 1 interaction.
    STRINGi9606.ENSP00000367373.

    Structurei

    3D structure databases

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

    Topological domain

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

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei698 – 71821HelicalSequence AnalysisAdd
    BLAST

    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.
    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. Align

    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

    MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ    50
    DLGLELAELV PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA 100
    ECSIHLELIA DRPLQVFHVE VKVKDINDNP PVFRGREQII FIPESRLLNS 150
    RFPIEGAADA DIGANALLTY TLSPSDYFSL DVEASDELSK SLWLELRKYL 200
    DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP LFDQAVYRVH 250
    LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG 300
    EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL 350
    AVTSLYLPIR EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST 400
    FKNYYSLVLD SALDRESLSV YELVVTARDG GSPSLWATAR VSVEVADVND 450
    NAPAFAQPEY TVFVKENNPP GCHIFTVSAR DADAQENALV SYSLVERRVG 500
    ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA GVPPLGSNVT 550
    LQVFVLDEND NAPALLAPRV GGTIGAVSEL VPRLVGAGHV VAKVRAVDAD 600
    SGYNAWLSYE LQPAAGGARI PFRVGLYTGE ISTTRVLDEA DLSRYRLLVL 650
    VKDHGEPALT ATATVLVSLV ESGQAPKASS RASVGVAGPE AALVDVNVYL 700
    IIAICAVSSL LVLTLLLYTA LRCSVPPTEG AYVPGKPTLV CSSALGSWSN 750
    SQQRRQRVCS SEGPPKTDLM AFSPGLSPSL NTSERNEQPE ANLDLSGNPR 800
    QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP TVSSATPEPE 850
    AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR 900
    QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ 950
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF152305 mRNA. Translation: AAD43699.1 .
    AF152479 mRNA. Translation: AAD43740.1 .
    AF169695 mRNA. Translation: AAF89692.1 .
    AC005609 Genomic DNA. Translation: AAC34325.1 .
    CCDSi CCDS54912.1. [Q9Y5I3-2 ]
    CCDS54913.1. [Q9Y5I3-1 ]
    RefSeqi NP_061723.1. NM_018900.3. [Q9Y5I3-1 ]
    NP_113598.1. NM_031410.2. [Q9Y5I3-3 ]
    NP_113599.1. NM_031411.2. [Q9Y5I3-2 ]
    UniGenei Hs.199343.

    3D structure databases

    ProteinModelPortali Q9Y5I3.
    SMRi Q9Y5I3. Positions 27-667.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q9Y5I3. 1 interaction.
    STRINGi 9606.ENSP00000367373.

    PTM databases

    PhosphoSitei Q9Y5I3.

    Polymorphism databases

    DMDMi 13878434.

    Proteomic databases

    PaxDbi Q9Y5I3.
    PRIDEi Q9Y5I3.

    Protocols and materials databases

    DNASUi 56147.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000378133 ; ENSP00000367373 ; ENSG00000204970 . [Q9Y5I3-3 ]
    ENST00000394633 ; ENSP00000378129 ; ENSG00000204970 . [Q9Y5I3-2 ]
    ENST00000504120 ; ENSP00000420840 ; ENSG00000204970 . [Q9Y5I3-1 ]
    GeneIDi 56147.
    KEGGi hsa:56147.
    UCSCi uc003lgz.3. human. [Q9Y5I3-3 ]
    uc003lha.2. human. [Q9Y5I3-2 ]
    uc003lhb.2. human. [Q9Y5I3-1 ]

    Organism-specific databases

    CTDi 56147.
    GeneCardsi GC05P140146.
    GC05P140147.
    H-InvDB HIX0032383.
    HGNCi HGNC:8663. PCDHA1.
    HPAi HPA008712.
    HPA035969.
    MIMi 604966. gene.
    606307. gene.
    neXtProti NX_Q9Y5I3.
    PharmGKBi PA33009.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG267459.
    HOGENOMi HOG000220892.
    HOVERGENi HBG054878.
    InParanoidi Q9Y5I3.
    KOi K16493.
    OMAi NEQPEAN.
    OrthoDBi EOG7KSX80.
    PhylomeDBi Q9Y5I3.
    TreeFami TF332299.

    Miscellaneous databases

    ChiTaRSi PCDHA1. human.
    GeneWikii Protocadherin_alpha_1.
    GenomeRNAii 56147.
    NextBioi 61750.
    PROi Q9Y5I3.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q9Y5I3.
    Genevestigatori Q9Y5I3.

    Family and domain databases

    Gene3Di 2.60.40.60. 6 hits.
    InterProi IPR002126. Cadherin.
    IPR015919. Cadherin-like.
    IPR020894. Cadherin_CS.
    IPR013164. Cadherin_N.
    [Graphical view ]
    Pfami PF00028. Cadherin. 5 hits.
    PF08266. Cadherin_2. 1 hit.
    [Graphical view ]
    PRINTSi PR00205. CADHERIN.
    SMARTi SM00112. CA. 6 hits.
    [Graphical view ]
    SUPFAMi SSF49313. SSF49313. 6 hits.
    PROSITEi PS00232. CADHERIN_1. 5 hits.
    PS50268. CADHERIN_2. 6 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 126 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