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Q9Y5F0

- PCDBD_HUMAN

UniProt

Q9Y5F0 - PCDBD_HUMAN

Protein

Protocadherin beta-13

Gene

PCDHB13

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 123 (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. calcium-dependent cell-cell adhesion Source: UniProtKB
    2. homophilic cell adhesion Source: InterPro
    3. synapse assembly Source: UniProtKB
    4. synaptic transmission Source: UniProtKB

    Keywords - Biological processi

    Cell adhesion

    Keywords - Ligandi

    Calcium

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protocadherin beta-13
    Short name:
    PCDH-beta-13
    Gene namesi
    Name:PCDHB13
    ORF Names:UNQ332/PRO531
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 5

    Organism-specific databases

    HGNCiHGNC:8684. PCDHB13.

    Subcellular locationi

    GO - Cellular componenti

    1. integral component of membrane Source: UniProtKB
    2. plasma membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cell membrane, Membrane

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA33029.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2828Sequence AnalysisAdd
    BLAST
    Chaini29 – 798770Protocadherin beta-13PRO_0000003938Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi418 – 4181N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi436 – 4361N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi567 – 5671N-linked (GlcNAc...)Sequence Analysis

    Keywords - PTMi

    Glycoprotein

    Proteomic databases

    PaxDbiQ9Y5F0.
    PRIDEiQ9Y5F0.

    PTM databases

    PhosphoSiteiQ9Y5F0.

    Expressioni

    Gene expression databases

    BgeeiQ9Y5F0.
    CleanExiHS_PCDHB13.
    GenevestigatoriQ9Y5F0.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9Y5F0.
    SMRiQ9Y5F0. Positions 33-679.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini29 – 690662ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini712 – 79887CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei691 – 71121HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini36 – 13499Cadherin 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini139 – 243105Cadherin 2PROSITE-ProRule annotationAdd
    BLAST
    Domaini248 – 348101Cadherin 3PROSITE-ProRule annotationAdd
    BLAST
    Domaini353 – 45199Cadherin 4PROSITE-ProRule annotationAdd
    BLAST
    Domaini456 – 561106Cadherin 5PROSITE-ProRule annotationAdd
    BLAST
    Domaini568 – 671104Cadherin 6PROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 6 cadherin domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat, Signal, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG323456.
    HOGENOMiHOG000220892.
    HOVERGENiHBG054878.
    InParanoidiQ9Y5F0.
    KOiK16494.
    OMAiNMTVLIA.
    OrthoDBiEOG7KSX80.
    PhylomeDBiQ9Y5F0.
    TreeFamiTF332299.

    Family and domain databases

    Gene3Di2.60.40.60. 5 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. 5 hits.
    PROSITEiPS00232. CADHERIN_1. 5 hits.
    PS50268. CADHERIN_2. 5 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q9Y5F0-1 [UniParc]FASTAAdd to Basket

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    MEASGKLICR QRQVLFSFLL LGLSLAGAAE PRSYSVVEET EGSSFVTNLA    50
    KDLGLEQREF SRRGVRVVSR GNKLHLQLNQ ETADLLLNEK LDREDLCGHT 100
    EPCVLRFQVL LESPFEFFQA ELQVIDINDH SPVFLDKQML VKVSESSPPG 150
    TTFPLKNAED LDVGQNNIEN YIISPNSYFR VLTRKRSDGR KYPELVLDKA 200
    LDREEEAELR LTLTALDGGS PPRSGTAQVY IEVLDVNDNA PEFEQPFYRV 250
    QISEDSPVGF LVVKVSATDV DTGVNGEISY SLFQASEEIG KTFKINPLTG 300
    EIELKKQLDF EKLQSYEVNI EARDAGTFSG KCTVLIQVID VNDHAPEVTM 350
    SAFTSPIPEN APETVVALFS VSDLDSGENG KISCSIQEDL PFLLKSAENF 400
    YTLLTERPLD RESRAEYNIT ITVTDLGTPM LITQLNMTVL IADVNDNAPA 450
    FTQTSYTLFV RENNSPALHI RSVSATDRDS GTNAQVTYSL LPPQDPHLPL 500
    TSLVSINADN GHLFALRSLD YEALQGFQFR VGASDHGSPA LSSEALVRVV 550
    VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA 600
    WLSYQLLKAT ELGLFGVWAH NGEVRTARLL SERDAAKHRL VVLVKDNGEP 650
    PRSATATLHV LLVDGFSQPY LPLPEAAPTQ AQADLLTVYL VVALASVSSL 700
    FLFSVLLFVA VRLCRRSRAA SVGRCLVPEG PLPGHLVDMS GTRTLSQSYQ 750
    YEVCLAGGSG TNEFKFLKPI IPNFPPQCPG KEIQGNSTFP NNFGFNIQ 798
    Length:798
    Mass (Da):87,552
    Last modified:November 1, 1999 - v1
    Checksum:i2A478554498B41A3
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti705 – 7051V → E in BAF85510. (PubMed:14702039)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti471 – 4711R → G.
    Corresponds to variant rs2910329 [ dbSNP | Ensembl ].
    VAR_059189

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF152492 mRNA. Translation: AAD43753.1.
    AF217745 mRNA. Translation: AAK51613.1.
    AY358427 mRNA. Translation: AAQ88793.1.
    AK292821 mRNA. Translation: BAF85510.1.
    BC033068 mRNA. Translation: AAH33068.1.
    BC051348 mRNA. Translation: AAH51348.1.
    BC071934 mRNA. Translation: AAH71934.1.
    CCDSiCCDS4255.1.
    RefSeqiNP_061756.1. NM_018933.3.
    UniGeneiHs.283803.

    Genome annotation databases

    EnsembliENST00000341948; ENSP00000345491; ENSG00000187372.
    GeneIDi56123.
    KEGGihsa:56123.
    UCSCiuc003lja.1. human.

    Polymorphism databases

    DMDMi13431381.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF152492 mRNA. Translation: AAD43753.1 .
    AF217745 mRNA. Translation: AAK51613.1 .
    AY358427 mRNA. Translation: AAQ88793.1 .
    AK292821 mRNA. Translation: BAF85510.1 .
    BC033068 mRNA. Translation: AAH33068.1 .
    BC051348 mRNA. Translation: AAH51348.1 .
    BC071934 mRNA. Translation: AAH71934.1 .
    CCDSi CCDS4255.1.
    RefSeqi NP_061756.1. NM_018933.3.
    UniGenei Hs.283803.

    3D structure databases

    ProteinModelPortali Q9Y5F0.
    SMRi Q9Y5F0. Positions 33-679.
    ModBasei Search...
    MobiDBi Search...

    PTM databases

    PhosphoSitei Q9Y5F0.

    Polymorphism databases

    DMDMi 13431381.

    Proteomic databases

    PaxDbi Q9Y5F0.
    PRIDEi Q9Y5F0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000341948 ; ENSP00000345491 ; ENSG00000187372 .
    GeneIDi 56123.
    KEGGi hsa:56123.
    UCSCi uc003lja.1. human.

    Organism-specific databases

    CTDi 56123.
    GeneCardsi GC05P141285.
    HGNCi HGNC:8684. PCDHB13.
    MIMi 604967. gene.
    606339. gene.
    neXtProti NX_Q9Y5F0.
    PharmGKBi PA33029.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG323456.
    HOGENOMi HOG000220892.
    HOVERGENi HBG054878.
    InParanoidi Q9Y5F0.
    KOi K16494.
    OMAi NMTVLIA.
    OrthoDBi EOG7KSX80.
    PhylomeDBi Q9Y5F0.
    TreeFami TF332299.

    Miscellaneous databases

    GeneWikii PCDHB13.
    GenomeRNAii 56123.
    NextBioi 35464687.
    PROi Q9Y5F0.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q9Y5F0.
    CleanExi HS_PCDHB13.
    Genevestigatori Q9Y5F0.

    Family and domain databases

    Gene3Di 2.60.40.60. 5 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. 5 hits.
    PROSITEi PS00232. CADHERIN_1. 5 hits.
    PS50268. CADHERIN_2. 5 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].
    2. "The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number."
      Vanhalst K., Kools P., Vanden Eynde E., van Roy F.
      FEBS Lett. 495:120-125(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    4. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Trachea.
    5. "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(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Lung and Prostate.

    Entry informationi

    Entry nameiPCDBD_HUMAN
    AccessioniPrimary (citable) accession number: Q9Y5F0
    Secondary accession number(s): A8K9V6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 27, 2001
    Last sequence update: November 1, 1999
    Last modified: October 1, 2014
    This is version 123 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