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Q62178

- SEM4A_MOUSE

UniProt

Q62178 - SEM4A_MOUSE

Protein

Semaphorin-4A

Gene

Sema4a

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 118 (01 Oct 2014)
      Sequence version 2 (27 Jul 2011)
      Previous versions | rss
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    Functioni

    Cell surface receptor for PLXNB1, PLXNB2, PLXNB3 and PLXND1 that plays an important role in cell-cell signaling. Plays a role in priming antigen-specific T-cells, promotes differentiation of Th1 T-helper cells, and thereby contributes to adaptive immunity. Promotes phosphorylation of TIMD2. Inhibits angiogenesis. Promotes axon growth cone collapse. Inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons.4 Publications

    GO - Molecular functioni

    1. receptor activity Source: InterPro

    GO - Biological processi

    1. angiogenesis Source: UniProtKB-KW
    2. axonogenesis Source: UniProtKB
    3. negative regulation of angiogenesis Source: UniProtKB
    4. regulation of cell shape Source: UniProtKB
    5. regulation of endothelial cell migration Source: UniProtKB
    6. semaphorin-plexin signaling pathway Source: UniProtKB
    7. T cell differentiation involved in immune response Source: UniProtKB
    8. T-helper 1 cell differentiation Source: UniProtKB

    Keywords - Molecular functioni

    Developmental protein

    Keywords - Biological processi

    Adaptive immunity, Angiogenesis, Differentiation, Immunity, Neurogenesis

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Semaphorin-4A
    Alternative name(s):
    Semaphorin-B
    Short name:
    Sema B
    Gene namesi
    Name:Sema4a
    Synonyms:Semab, SemB
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 3

    Organism-specific databases

    MGIiMGI:107560. Sema4a.

    Subcellular locationi

    Cell membrane 4 Publications; Single-pass type I membrane protein 4 Publications

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Cell membrane, Membrane

    Pathology & Biotechi

    Disruption phenotypei

    Results are contradictory; one study (PubMed:15780988) finds no visible phenotype; mice are born at the expected Mendelian ratio and are fertile, but they present defects in T-cell differentiation and in T-cell responses to antigens. According to another publication (PubMed:15277503) gene disruption leads to degeneration of photoreceptor cells in the retina within the first month of life.3 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 3232Sequence AnalysisAdd
    BLAST
    Chaini33 – 760728Semaphorin-4APRO_0000032323Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi113 ↔ 124PROSITE-ProRule annotation
    Glycosylationi120 – 1201N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi135 – 1351N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi142 ↔ 151PROSITE-ProRule annotation
    Disulfide bondi269 ↔ 379PROSITE-ProRule annotation
    Disulfide bondi293 ↔ 339PROSITE-ProRule annotation
    Glycosylationi496 – 4961N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi497 ↔ 514PROSITE-ProRule annotation
    Disulfide bondi506 ↔ 523PROSITE-ProRule annotation
    Disulfide bondi579 ↔ 623PROSITE-ProRule annotation
    Glycosylationi606 – 6061N-linked (GlcNAc...)Sequence Analysis

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Proteomic databases

    MaxQBiQ62178.
    PaxDbiQ62178.
    PRIDEiQ62178.

    PTM databases

    PhosphoSiteiQ62178.

    Expressioni

    Developmental stagei

    Expressed from day 10 in the embryo. Low levels found between days 10-12. Expression peaks on day 13 with moderate levels from then until birth.

    Gene expression databases

    ArrayExpressiQ62178.
    BgeeiQ62178.
    GenevestigatoriQ62178.

    Interactioni

    Subunit structurei

    Interacts with PLXNB1, PLXNB2, PLXNB3 and PLXND1. Probable ligand for TIMD2.3 Publications

    Protein-protein interaction databases

    STRINGi10090.ENSMUSP00000029700.

    Structurei

    3D structure databases

    ProteinModelPortaliQ62178.
    SMRiQ62178. Positions 37-627.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini33 – 682650ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini704 – 76057CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei683 – 70321HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini36 – 494459SemaPROSITE-ProRule annotationAdd
    BLAST
    Domaini496 – 54752PSIAdd
    BLAST
    Domaini572 – 63059Ig-like C2-typeAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi609 – 6124Poly-Leu

    Sequence similaritiesi

    Belongs to the semaphorin family.Curated
    Contains 1 PSI domain.Curated
    Contains 1 Sema domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG287504.
    GeneTreeiENSGT00560000076864.
    HOGENOMiHOG000116087.
    HOVERGENiHBG061165.
    KOiK06521.
    OMAiFAFSPAC.
    OrthoDBiEOG7H791Q.
    PhylomeDBiQ62178.
    TreeFamiTF316102.

    Family and domain databases

    Gene3Di2.130.10.10. 1 hit.
    InterProiIPR016201. Plexin-like_fold.
    IPR002165. Plexin_repeat.
    IPR001627. Semap_dom.
    IPR027231. Semaphorin.
    IPR015943. WD40/YVTN_repeat-like_dom.
    [Graphical view]
    PANTHERiPTHR11036. PTHR11036. 1 hit.
    PfamiPF01437. PSI. 1 hit.
    PF01403. Sema. 1 hit.
    [Graphical view]
    SMARTiSM00423. PSI. 1 hit.
    SM00630. Sema. 1 hit.
    [Graphical view]
    SUPFAMiSSF101912. SSF101912. 1 hit.
    SSF103575. SSF103575. 1 hit.
    PROSITEiPS51004. SEMA. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q62178-1 [UniParc]FASTAAdd to Basket

    « Hide

    MALPSLGQDS WSLLRVFFFQ LFLLPSLPPA SGTGGQGPMP RVKYHAGDGH    50
    RALSFFQQKG LRDFDTLLLS DDGNTLYVGA REAVLALNIQ NPGIPRLKNM 100
    IPWPASERKK TECAFKKKSN ETQCFNFIRV LVSYNATHLY ACGTFAFSPA 150
    CTFIELQDSL LLPILIDKVM DGKGQSPFDP VHKHTAVLVD GMLYSGTMNN 200
    FLGSEPILMR TLGSQPVLKT DIFLRWLHAD ASFVAAIPST QVVYFFFEET 250
    ASEFDFFEEL YISRVAQVCK NDVGGEKLLQ KKWTTFLKAQ LLCAQPGQLP 300
    FNIIRHAVLL PADSPSVSRI YAVFTSQWQV GGTRSSAVCA FSLTDIERVF 350
    KGKYKELNKE TSRWTTYRGS EVSPRPGSCS MGPSSDKALT FMKDHFLMDE 400
    HVVGTPLLVK SGVEYTRLAV ESARGLDGSS HVVMYLGTST GSLHKAVVPQ 450
    DSSAYLVEEI QLSPDSEPVR NLQLAPAQGA VFAGFSGGIW RVPRANCSVY 500
    ESCVDCVLAR DPHCAWDPES RLCSLLSGST KPWKQDMERG NPEWVCTRGP 550
    MARSPRRQSP PQLIKEVLTV PNSILELPCP HLSALASYHW SHGRAKISEA 600
    SATVYNGSLL LLPQDGVGGL YQCVATENGY SYPVVSYWVD SQDQPLALDP 650
    ELAGVPRERV QVPLTRVGGG ASMAAQRSYW PHFLIVTVLL AIVLLGVLTL 700
    LLASPLGALR ARGKVQGCGM LPPREKAPLS RDQHLQPSKD HRTSASDVDA 750
    DNNHLGAEVA 760
    Length:760
    Mass (Da):83,421
    Last modified:July 27, 2011 - v2
    Checksum:iC13BD31BD90BE3D9
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti83 – 831A → T in CAA59983. (PubMed:7748561)Curated
    Sequence conflicti178 – 1858FDPVHKHT → LTLFTSTQ in CAA59983. (PubMed:7748561)Curated
    Sequence conflicti215 – 2151Q → H in CAA59983. (PubMed:7748561)Curated
    Sequence conflicti442 – 4421S → P in CAA59983. (PubMed:7748561)Curated
    Sequence conflicti578 – 5781P → R in CAA59983. (PubMed:7748561)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X85991 mRNA. Translation: CAA59983.1.
    AC102388 Genomic DNA. No translation available.
    CH466547 Genomic DNA. Translation: EDL15277.1.
    CH466547 Genomic DNA. Translation: EDL15278.1.
    CH466547 Genomic DNA. Translation: EDL15279.1.
    CCDSiCCDS17475.1.
    PIRiI48745.
    RefSeqiNP_001156961.1. NM_001163489.1.
    NP_001156962.1. NM_001163490.1.
    NP_001156963.1. NM_001163491.1.
    NP_038686.3. NM_013658.3.
    XP_006501252.1. XM_006501189.1.
    UniGeneiMm.439752.

    Genome annotation databases

    EnsembliENSMUST00000029700; ENSMUSP00000029700; ENSMUSG00000028064.
    ENSMUST00000165898; ENSMUSP00000128510; ENSMUSG00000028064.
    ENSMUST00000166237; ENSMUSP00000125909; ENSMUSG00000028064.
    ENSMUST00000169222; ENSMUSP00000128887; ENSMUSG00000028064.
    GeneIDi20351.
    KEGGimmu:20351.
    UCSCiuc008pvg.2. mouse.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X85991 mRNA. Translation: CAA59983.1 .
    AC102388 Genomic DNA. No translation available.
    CH466547 Genomic DNA. Translation: EDL15277.1 .
    CH466547 Genomic DNA. Translation: EDL15278.1 .
    CH466547 Genomic DNA. Translation: EDL15279.1 .
    CCDSi CCDS17475.1.
    PIRi I48745.
    RefSeqi NP_001156961.1. NM_001163489.1.
    NP_001156962.1. NM_001163490.1.
    NP_001156963.1. NM_001163491.1.
    NP_038686.3. NM_013658.3.
    XP_006501252.1. XM_006501189.1.
    UniGenei Mm.439752.

    3D structure databases

    ProteinModelPortali Q62178.
    SMRi Q62178. Positions 37-627.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 10090.ENSMUSP00000029700.

    PTM databases

    PhosphoSitei Q62178.

    Proteomic databases

    MaxQBi Q62178.
    PaxDbi Q62178.
    PRIDEi Q62178.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000029700 ; ENSMUSP00000029700 ; ENSMUSG00000028064 .
    ENSMUST00000165898 ; ENSMUSP00000128510 ; ENSMUSG00000028064 .
    ENSMUST00000166237 ; ENSMUSP00000125909 ; ENSMUSG00000028064 .
    ENSMUST00000169222 ; ENSMUSP00000128887 ; ENSMUSG00000028064 .
    GeneIDi 20351.
    KEGGi mmu:20351.
    UCSCi uc008pvg.2. mouse.

    Organism-specific databases

    CTDi 64218.
    MGIi MGI:107560. Sema4a.

    Phylogenomic databases

    eggNOGi NOG287504.
    GeneTreei ENSGT00560000076864.
    HOGENOMi HOG000116087.
    HOVERGENi HBG061165.
    KOi K06521.
    OMAi FAFSPAC.
    OrthoDBi EOG7H791Q.
    PhylomeDBi Q62178.
    TreeFami TF316102.

    Miscellaneous databases

    ChiTaRSi SEMA4A. mouse.
    NextBioi 298207.
    PROi Q62178.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q62178.
    Bgeei Q62178.
    Genevestigatori Q62178.

    Family and domain databases

    Gene3Di 2.130.10.10. 1 hit.
    InterProi IPR016201. Plexin-like_fold.
    IPR002165. Plexin_repeat.
    IPR001627. Semap_dom.
    IPR027231. Semaphorin.
    IPR015943. WD40/YVTN_repeat-like_dom.
    [Graphical view ]
    PANTHERi PTHR11036. PTHR11036. 1 hit.
    Pfami PF01437. PSI. 1 hit.
    PF01403. Sema. 1 hit.
    [Graphical view ]
    SMARTi SM00423. PSI. 1 hit.
    SM00630. Sema. 1 hit.
    [Graphical view ]
    SUPFAMi SSF101912. SSF101912. 1 hit.
    SSF103575. SSF103575. 1 hit.
    PROSITEi PS51004. SEMA. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Murine semaphorin D/collapsin is a member of a diverse gene family and creates domains inhibitory for axonal extension."
      Pueschel A.W., Adams R.H., Betz H.
      Neuron 14:941-948(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: NMRI.
      Tissue: Brain.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: C57BL/6J.
    3. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
      Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "Class IV semaphorin Sema4A enhances T-cell activation and interacts with Tim-2."
      Kumanogoh A., Marukawa S., Suzuki K., Takegahara N., Watanabe C., Ch'ng E., Ishida I., Fujimura H., Sakoda S., Yoshida K., Kikutani H.
      Nature 419:629-633(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH TIMD2.
    5. Cited for: DISRUPTION PHENOTYPE.
    6. Cited for: DISRUPTION PHENOTYPE, SUBCELLULAR LOCATION, FUNCTION.
    7. "Semaphorin-4A, an activator for T-cell-mediated immunity, suppresses angiogenesis via plexin-D1."
      Toyofuku T., Yabuki M., Kamei J., Kamei M., Makino N., Kumanogoh A., Hori M.
      EMBO J. 26:1373-1384(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE, FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH PLXND1.
    8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Liver.
    9. "The phagosomal proteome in interferon-gamma-activated macrophages."
      Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
      Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    10. "Sema4A induces cell morphological changes through B-type plexin-mediated signaling."
      Yukawa K., Tanaka T., Yoshida K., Takeuchi N., Ito T., Takamatsu H., Kikutani H., Kumanogoh A.
      Int. J. Mol. Med. 25:225-230(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH PLXNB1; PLXNB2 AND PLXNB3.

    Entry informationi

    Entry nameiSEM4A_MOUSE
    AccessioniPrimary (citable) accession number: Q62178
    Secondary accession number(s): D3Z5L2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: July 27, 2011
    Last modified: October 1, 2014
    This is version 118 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

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

    External Data

    Dasty 3