Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

O88689

- PCDA4_MOUSE

UniProt

O88689 - PCDA4_MOUSE

Protein

Protocadherin alpha-4

Gene

Pcdha4

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 100 (01 Oct 2014)
      Sequence version 1 (01 Nov 1998)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    Functioni

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

    GO - Molecular functioni

    1. calcium ion binding Source: InterPro

    GO - Biological processi

    1. homophilic cell adhesion Source: InterPro

    Keywords - Biological processi

    Cell adhesion

    Keywords - Ligandi

    Calcium

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protocadherin alpha-4
    Short name:
    PCDH-alpha-4
    Gene namesi
    Name:Pcdha4
    Synonyms:Cnr1
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 18

    Organism-specific databases

    MGIiMGI:1298406. Pcdha4.

    Subcellular locationi

    Cell membrane 1 Publication; Single-pass type I membrane protein 1 Publication
    Note: Detected in dendrites and synapses.

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Cell membrane, Membrane

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2929Sequence AnalysisAdd
    BLAST
    Chaini30 – 947918Protocadherin alpha-4PRO_0000240663Add
    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

    PaxDbiO88689.
    PRIDEiO88689.

    PTM databases

    PhosphoSiteiO88689.

    Expressioni

    Tissue specificityi

    Detected in brain throughout embryonic development. Detected in adult brain, in particular in cerebellum and forebrain.1 Publication

    Gene expression databases

    ArrayExpressiO88689.
    BgeeiO88689.
    CleanExiMM_CNR1.
    MM_PCDHA4.
    GenevestigatoriO88689.

    Interactioni

    Subunit structurei

    Interacts with FYN.1 Publication

    Protein-protein interaction databases

    DIPiDIP-41020N.
    MINTiMINT-113982.

    Structurei

    Secondary structure

    1
    947
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi30 – 389
    Helixi48 – 525
    Helixi56 – 594
    Turni60 – 634
    Beta strandi74 – 774
    Turni79 – 813
    Beta strandi84 – 863
    Helixi92 – 954
    Beta strandi97 – 1015
    Beta strandi103 – 1108
    Turni111 – 1144
    Beta strandi115 – 12410

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1WUZNMR-A27-129[»]
    ProteinModelPortaliO88689.
    SMRiO88689. Positions 27-667.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO88689.

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini30 – 697668ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini719 – 947229CytoplasmicSequence 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
    Domaini134 – 242109Cadherin 2PROSITE-ProRule annotationAdd
    BLAST
    Domaini243 – 350108Cadherin 3PROSITE-ProRule annotationAdd
    BLAST
    Domaini351 – 455105Cadherin 4PROSITE-ProRule annotationAdd
    BLAST
    Domaini456 – 565110Cadherin 5PROSITE-ProRule annotationAdd
    BLAST
    Domaini573 – 681109Cadherin 6PROSITE-ProRule annotationAdd
    BLAST
    Repeati734 – 7374PXXP 1
    Repeati774 – 7774PXXP 2
    Repeati796 – 7994PXXP 3
    Repeati829 – 8324PXXP 4
    Repeati870 – 8734PXXP 5
    Repeati888 – 8914PXXP 6

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni734 – 8911586 X 4 AA repeats of P-X-X-PAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi920 – 9278Poly-Lys

    Sequence similaritiesi

    Contains 6 cadherin domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat, Signal, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG267459.
    GeneTreeiENSGT00750000117438.
    HOGENOMiHOG000220892.
    HOVERGENiHBG054878.
    KOiK16493.

    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

    Isoform 1 (identifier: O88689-1) [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

    MEFSWGSGQE SQRLLLSFLL LAIWEAGNSQ IHYSIPEEAK HGTFVGRIAQ    50
    DLGLELTELV PRLFRVASKD RGDLLEVNLQ NGILFVNSRI DREELCGRSA 100
    ECSIHLEVIV DRPLQVFHVE VEVRDINDNP PRFPTTQKNL FIAESRPLDT 150
    WFPLEGASDA DIGINAVLTY RLSPNDYFSL EKPSNDERVK GLGLVLRKSL 200
    DREETPEIIL VLTVTDGGKP ELTGSVQLLI TVLDANDNAP VFDRSLYTVK 250
    LPENVPNGTL VVKVNASDLD EGVNGDIMYS FSTDISPNVK YKFHIDPVSG 300
    EIIVKGYIDF EECKSYEILI EGIDKGQLPL SGHCKVIVQV EDINDNVPEL 350
    EFKSLSLPIR ENSPVGTVIA LISVSDRDTG VNGQVTCSLT SHVPFKLVST 400
    FKNYYSLVLD SALDRETTAD YKVVVTARDG GSPSLWATAS VSVEVADVND 450
    NAPVFAQPEY TVFVKENNPP GAHIFTVSAM DADAQENALV SYSLVERRVG 500
    ERLLSSYVSV HAESGKVFAL QPLDHEELEL LRFQVSARDA GVPALGSNVT 550
    LQVFVLDEND NAPTLLEPEA GVSGGIVSRL VSRSVGAGHV VAKVRAVDAD 600
    SGYNAWLSYE LQSSEGNSRS LFRVGLYTGE ISTTRILDEA DSPRQRLLVL 650
    VKDHGDPAMI VTATVLVSLV ENGPVPKAPS RVSTSVTHSE ASLVDVNVYL 700
    IIAICAVSSL LVLTLLLYTA LRCSTVPSES VCGPPKPVMV CSSAVGSWSY 750
    SQQRRQRVCS GEYPPKTDLM AFSPSLSDSR DREDQLQSAE DSSGKPRQPN 800
    PDWRYSASLR AGMHSSVHLE EAGILRAGPG GPDQQWPTVS SATPEPEAGE 850
    VSPPVGAGVN SNSWTFKYGP GNPKQSGPGE LPDKFIIPGS PAIISIRQEP 900
    ANNQIDKSDF ITFGKKEETK KKKKKKKGNK TQEKKEKGNS TTDNSDQ 947
    Length:947
    Mass (Da):103,143
    Last modified:November 1, 1998 - v1
    Checksum:i082497DBBAEFB503
    GO
    Isoform 2 (identifier: O88689-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         535-795: Missing.
         879-947: GELPDKFIIP...GNSTTDNSDQ → EPKKQTQVSFLPRRKGEASQPRQ

    Show »
    Length:640
    Mass (Da):70,430
    Checksum:i7B8393620F457915
    GO
    Isoform 3 (identifier: O88689-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         796-947: PRQPNPDWRY...GNSTTDNSDQ → QAPPNTDWRF...KKKSGKKEKK

    Show »
    Length:919
    Mass (Da):99,666
    Checksum:i21D65CCE53617EB5
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei535 – 795261Missing in isoform 2. 1 PublicationVSP_019413Add
    BLAST
    Alternative sequencei796 – 947152PRQPN…DNSDQ → QAPPNTDWRFSQAQRPGTSG SQNGDETGTWPNNQFDTEML QAMILASASEAADGSSTLGG GAGTMGLSARYGPQFTLQHV PDYRQNVYIPGSNATLTNAA GKRDGKAPAGGNGNKKKSGK KEKK in isoform 3. 1 PublicationVSP_019414Add
    BLAST
    Alternative sequencei879 – 94769GELPD…DNSDQ → EPKKQTQVSFLPRRKGEASQ PRQ in isoform 2. 1 PublicationVSP_019415Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D86916 mRNA. Translation: BAA29045.1.
    AY013762 mRNA. Translation: AAK26051.1.
    AF464178 Genomic DNA. Translation: AAM93577.1.
    AF464180 mRNA. Translation: AAM93579.1.
    BC060211 mRNA. Translation: AAH60211.1.
    AK149282 mRNA. Translation: BAE28788.1.
    CCDSiCCDS37776.1. [O88689-1]
    RefSeqiNP_001167625.1. NM_001174154.1. [O88689-3]
    NP_031792.1. NM_007766.2. [O88689-1]
    UniGeneiMm.308500.

    Genome annotation databases

    EnsembliENSMUST00000115661; ENSMUSP00000111325; ENSMUSG00000007440. [O88689-1]
    GeneIDi100384868.
    12936.
    KEGGimmu:100384868.
    mmu:12936.
    UCSCiuc008eox.2. mouse. [O88689-1]
    uc008eoy.1. mouse. [O88689-3]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D86916 mRNA. Translation: BAA29045.1 .
    AY013762 mRNA. Translation: AAK26051.1 .
    AF464178 Genomic DNA. Translation: AAM93577.1 .
    AF464180 mRNA. Translation: AAM93579.1 .
    BC060211 mRNA. Translation: AAH60211.1 .
    AK149282 mRNA. Translation: BAE28788.1 .
    CCDSi CCDS37776.1. [O88689-1 ]
    RefSeqi NP_001167625.1. NM_001174154.1. [O88689-3 ]
    NP_031792.1. NM_007766.2. [O88689-1 ]
    UniGenei Mm.308500.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1WUZ NMR - A 27-129 [» ]
    ProteinModelPortali O88689.
    SMRi O88689. Positions 27-667.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-41020N.
    MINTi MINT-113982.

    PTM databases

    PhosphoSitei O88689.

    Proteomic databases

    PaxDbi O88689.
    PRIDEi O88689.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000115661 ; ENSMUSP00000111325 ; ENSMUSG00000007440 . [O88689-1 ]
    GeneIDi 100384868.
    12936.
    KEGGi mmu:100384868.
    mmu:12936.
    UCSCi uc008eox.2. mouse. [O88689-1 ]
    uc008eoy.1. mouse. [O88689-3 ]

    Organism-specific databases

    CTDi 100384868.
    56144.
    MGIi MGI:1298406. Pcdha4.

    Phylogenomic databases

    eggNOGi NOG267459.
    GeneTreei ENSGT00750000117438.
    HOGENOMi HOG000220892.
    HOVERGENi HBG054878.
    KOi K16493.

    Miscellaneous databases

    EvolutionaryTracei O88689.
    NextBioi 282614.
    PROi O88689.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O88689.
    Bgeei O88689.
    CleanExi MM_CNR1.
    MM_PCDHA4.
    Genevestigatori O88689.

    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. "Diversity revealed by a novel family of cadherins expressed in neurons at a synaptic complex."
      Kohmura N., Senzaki K., Hamada S., Kai N., Yasuda R., Watanabe M., Ishii H., Yasuda M., Mishina M., Yagi T.
      Neuron 20:1137-1151(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH FYN, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
      Strain: C57BL/6J.
      Tissue: Brain.
    2. "Comparative DNA sequence analysis of mouse and human protocadherin gene clusters."
      Wu Q., Zhang T., Cheng J.-F., Kim Y., Grimwood J., Schmutz J., Dickson M., Noonan J.P., Zhang M.Q., Myers R.M., Maniatis T.
      Genome Res. 11:389-404(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Tissue: Brain.
    3. "Molecular mechanisms governing Pcdh-gamma gene expression: evidence for a multiple promoter and cis-alternative splicing model."
      Wang X., Su H., Bradley A.
      Genes Dev. 16:1890-1905(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] (ISOFORM 3).
      Strain: C57BL/6J.
    4. "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] (ISOFORM 2).
      Strain: C57BL/6.
      Tissue: Brain.
    5. "The transcriptional landscape of the mammalian genome."
      Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
      , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
      Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-919 (ISOFORM 1).
      Strain: C57BL/6J.
      Tissue: Retina.
    6. "1H, 13C and 15N resonance assignments of the first cadherin domain of cadherin-related neuronal receptor (CNR)/protocadherin alpha."
      Umitsu M., Morishita H., Murata Y., Udaka K., Akutsu H., Yagi T., Ikegami T.
      J. Biomol. NMR 31:365-366(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 27-129.

    Entry informationi

    Entry nameiPCDA4_MOUSE
    AccessioniPrimary (citable) accession number: O88689
    Secondary accession number(s): Q3UEX3
    , Q6PAM9, Q8K487, Q8K489
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 27, 2006
    Last sequence update: November 1, 1998
    Last modified: October 1, 2014
    This is version 100 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. MGD cross-references
      Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3