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Q9Y279

- VSIG4_HUMAN

UniProt

Q9Y279 - VSIG4_HUMAN

Protein

V-set and immunoglobulin domain-containing protein 4

Gene

VSIG4

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein 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

    Phagocytic receptor, strong negative regulator of T-cell proliferation and IL2 production. Potent inhibitor of the alternative complement pathway convertases.2 Publications

    GO - Molecular functioni

    1. protein binding Source: IntAct

    GO - Biological processi

    1. complement activation, alternative pathway Source: UniProtKB-KW
    2. negative regulation of interleukin-2 production Source: Ensembl
    3. negative regulation of T cell proliferation Source: Ensembl

    Keywords - Biological processi

    Complement alternate pathway, Immunity, Innate immunity

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    V-set and immunoglobulin domain-containing protein 4
    Alternative name(s):
    Protein Z39Ig
    Gene namesi
    Name:VSIG4
    Synonyms:CRIg, Z39IG
    ORF Names:UNQ317/PRO362
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome X

    Organism-specific databases

    HGNCiHGNC:17032. VSIG4.

    Subcellular locationi

    GO - Cellular componenti

    1. extracellular vesicular exosome Source: UniProt
    2. integral component of membrane Source: UniProtKB-KW

    Keywords - Cellular componenti

    Membrane

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA134986421.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 19191 PublicationAdd
    BLAST
    Chaini20 – 399380V-set and immunoglobulin domain-containing protein 4PRO_0000015006Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi41 ↔ 1131 PublicationPROSITE-ProRule annotation
    Disulfide bondi165 ↔ 211PROSITE-ProRule annotation

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PaxDbiQ9Y279.
    PRIDEiQ9Y279.

    PTM databases

    PhosphoSiteiQ9Y279.

    Expressioni

    Tissue specificityi

    Abundantly expressed in several fetal tissues. In adult tissues, highest expression in lung and placenta. Expressed in resting macrophages.2 Publications

    Gene expression databases

    ArrayExpressiQ9Y279.
    BgeeiQ9Y279.
    CleanExiHS_VSIG4.
    GenevestigatoriQ9Y279.

    Organism-specific databases

    HPAiCAB026000.
    HPA003903.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    C3P010245EBI-903144,EBI-905851

    Protein-protein interaction databases

    BioGridi116455. 3 interactions.
    IntActiQ9Y279. 2 interactions.
    STRINGi9606.ENSP00000363869.

    Structurei

    Secondary structure

    1
    399
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi27 – 326
    Beta strandi37 – 393
    Beta strandi50 – 589
    Beta strandi60 – 634
    Beta strandi65 – 717
    Beta strandi74 – 774
    Helixi80 – 823
    Turni83 – 853
    Beta strandi86 – 883
    Beta strandi98 – 1003
    Helixi105 – 1073
    Beta strandi109 – 11810
    Beta strandi124 – 13613

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ICCX-ray1.20A19-137[»]
    2ICEX-ray3.10S/T19-137[»]
    2ICFX-ray4.10S19-137[»]
    ProteinModelPortaliQ9Y279.
    SMRiQ9Y279. Positions 19-236.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9Y279.

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini20 – 283264ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini305 – 39995CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei284 – 30421HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini21 – 131111Ig-like 1Add
    BLAST
    Domaini143 – 22684Ig-like 2Add
    BLAST

    Sequence similaritiesi

    Keywords - Domaini

    Immunoglobulin domain, Repeat, Signal, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG39012.
    HOGENOMiHOG000137602.
    HOVERGENiHBG055008.
    InParanoidiQ9Y279.
    OMAiTYGHPIL.
    PhylomeDBiQ9Y279.
    TreeFamiTF336175.

    Family and domain databases

    Gene3Di2.60.40.10. 2 hits.
    InterProiIPR007110. Ig-like_dom.
    IPR013783. Ig-like_fold.
    IPR003599. Ig_sub.
    IPR003598. Ig_sub2.
    IPR013106. Ig_V-set.
    [Graphical view]
    PfamiPF07686. V-set. 1 hit.
    [Graphical view]
    SMARTiSM00409. IG. 1 hit.
    SM00408. IGc2. 1 hit.
    [Graphical view]
    PROSITEiPS50835. IG_LIKE. 2 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: Q9Y279-1) [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

    MGILLGLLLL GHLTVDTYGR PILEVPESVT GPWKGDVNLP CTYDPLQGYT    50
    QVLVKWLVQR GSDPVTIFLR DSSGDHIQQA KYQGRLHVSH KVPGDVSLQL 100
    STLEMDDRSH YTCEVTWQTP DGNQVVRDKI TELRVQKLSV SKPTVTTGSG 150
    YGFTVPQGMR ISLQCQARGS PPISYIWYKQ QTNNQEPIKV ATLSTLLFKP 200
    AVIADSGSYF CTAKGQVGSE QHSDIVKFVV KDSSKLLKTK TEAPTTMTYP 250
    LKATSTVKQS WDWTTDMDGY LGETSAGPGK SLPVFAIILI ISLCCMVVFT 300
    MAYIMLCRKT SQQEHVYEAA RAHAREANDS GETMRVAIFA SGCSSDEPTS 350
    QNLGNNYSDE PCIGQEYQII AQINGNYARL LDTVPLDYEF LATEGKSVC 399
    Length:399
    Mass (Da):43,987
    Last modified:November 1, 1999 - v1
    Checksum:i735CA3BC58185035
    GO
    Isoform 2 (identifier: Q9Y279-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         322-399: Missing.

    Note: No experimental confirmation available.

    Show »
    Length:321
    Mass (Da):35,544
    Checksum:iB2AB2E3151D39C6E
    GO
    Isoform 3 (identifier: Q9Y279-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         138-232: LSVSKPTVTT...SDIVKFVVKD → H

    Show »
    Length:305
    Mass (Da):33,857
    Checksum:i12C57C74CCD69134
    GO

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti108 – 1081R → W.
    Corresponds to variant rs34581041 [ dbSNP | Ensembl ].
    VAR_049956
    Natural varianti272 – 2721G → E.
    Corresponds to variant rs34222730 [ dbSNP | Ensembl ].
    VAR_049957
    Natural varianti279 – 2791G → E.
    Corresponds to variant rs17315645 [ dbSNP | Ensembl ].
    VAR_049958
    Natural varianti397 – 3971S → I.
    Corresponds to variant rs35553694 [ dbSNP | Ensembl ].
    VAR_049959

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei138 – 23295LSVSK…FVVKD → H in isoform 3. 1 PublicationVSP_041213Add
    BLAST
    Alternative sequencei322 – 39978Missing in isoform 2. 1 PublicationVSP_012813Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ132502 mRNA. Translation: CAB51536.1.
    AY358341 mRNA. Translation: AAQ88707.1.
    AL034397 Genomic DNA. Translation: CAB46921.1.
    CR607860 mRNA. No translation available.
    BC010525 mRNA. Translation: AAH10525.1.
    CCDSiCCDS14383.1. [Q9Y279-1]
    CCDS48132.1. [Q9Y279-3]
    CCDS55435.1. [Q9Y279-2]
    RefSeqiNP_001093901.1. NM_001100431.1. [Q9Y279-3]
    NP_001171759.1. NM_001184830.1. [Q9Y279-2]
    NP_001171760.1. NM_001184831.1.
    NP_001244332.1. NM_001257403.1.
    NP_009199.1. NM_007268.2. [Q9Y279-1]
    UniGeneiHs.8904.

    Genome annotation databases

    EnsembliENST00000374737; ENSP00000363869; ENSG00000155659. [Q9Y279-1]
    ENST00000412866; ENSP00000394143; ENSG00000155659. [Q9Y279-3]
    ENST00000455586; ENSP00000411581; ENSG00000155659. [Q9Y279-2]
    GeneIDi11326.
    KEGGihsa:11326.
    UCSCiuc004dwh.2. human. [Q9Y279-1]
    uc004dwi.2. human. [Q9Y279-3]

    Polymorphism databases

    DMDMi59799152.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ132502 mRNA. Translation: CAB51536.1 .
    AY358341 mRNA. Translation: AAQ88707.1 .
    AL034397 Genomic DNA. Translation: CAB46921.1 .
    CR607860 mRNA. No translation available.
    BC010525 mRNA. Translation: AAH10525.1 .
    CCDSi CCDS14383.1. [Q9Y279-1 ]
    CCDS48132.1. [Q9Y279-3 ]
    CCDS55435.1. [Q9Y279-2 ]
    RefSeqi NP_001093901.1. NM_001100431.1. [Q9Y279-3 ]
    NP_001171759.1. NM_001184830.1. [Q9Y279-2 ]
    NP_001171760.1. NM_001184831.1.
    NP_001244332.1. NM_001257403.1.
    NP_009199.1. NM_007268.2. [Q9Y279-1 ]
    UniGenei Hs.8904.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2ICC X-ray 1.20 A 19-137 [» ]
    2ICE X-ray 3.10 S/T 19-137 [» ]
    2ICF X-ray 4.10 S 19-137 [» ]
    ProteinModelPortali Q9Y279.
    SMRi Q9Y279. Positions 19-236.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 116455. 3 interactions.
    IntActi Q9Y279. 2 interactions.
    STRINGi 9606.ENSP00000363869.

    PTM databases

    PhosphoSitei Q9Y279.

    Polymorphism databases

    DMDMi 59799152.

    Proteomic databases

    PaxDbi Q9Y279.
    PRIDEi Q9Y279.

    Protocols and materials databases

    DNASUi 11326.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000374737 ; ENSP00000363869 ; ENSG00000155659 . [Q9Y279-1 ]
    ENST00000412866 ; ENSP00000394143 ; ENSG00000155659 . [Q9Y279-3 ]
    ENST00000455586 ; ENSP00000411581 ; ENSG00000155659 . [Q9Y279-2 ]
    GeneIDi 11326.
    KEGGi hsa:11326.
    UCSCi uc004dwh.2. human. [Q9Y279-1 ]
    uc004dwi.2. human. [Q9Y279-3 ]

    Organism-specific databases

    CTDi 11326.
    GeneCardsi GC0XM065241.
    HGNCi HGNC:17032. VSIG4.
    HPAi CAB026000.
    HPA003903.
    MIMi 300353. gene.
    neXtProti NX_Q9Y279.
    PharmGKBi PA134986421.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG39012.
    HOGENOMi HOG000137602.
    HOVERGENi HBG055008.
    InParanoidi Q9Y279.
    OMAi TYGHPIL.
    PhylomeDBi Q9Y279.
    TreeFami TF336175.

    Miscellaneous databases

    EvolutionaryTracei Q9Y279.
    GenomeRNAii 11326.
    NextBioi 43025.
    PROi Q9Y279.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9Y279.
    Bgeei Q9Y279.
    CleanExi HS_VSIG4.
    Genevestigatori Q9Y279.

    Family and domain databases

    Gene3Di 2.60.40.10. 2 hits.
    InterProi IPR007110. Ig-like_dom.
    IPR013783. Ig-like_fold.
    IPR003599. Ig_sub.
    IPR003598. Ig_sub2.
    IPR013106. Ig_V-set.
    [Graphical view ]
    Pfami PF07686. V-set. 1 hit.
    [Graphical view ]
    SMARTi SM00409. IG. 1 hit.
    SM00408. IGc2. 1 hit.
    [Graphical view ]
    PROSITEi PS50835. IG_LIKE. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Cloning of Z39Ig, a novel gene with immunoglobulin-like domains located on human chromosome X."
      Langnaese K., Colleaux L., Kloos D.U., Fontes M., Wieacker P.
      Biochim. Biophys. Acta 1492:522-525(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    3. "Full-length cDNA libraries and normalization."
      Li W.B., Gruber C., Jessee J., Polayes D.
      Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
      Tissue: Placenta.
    4. "The DNA sequence of the human X chromosome."
      Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
      , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
      Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    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] (ISOFORM 1).
      Tissue: Brain.
    6. "Signal peptide prediction based on analysis of experimentally verified cleavage sites."
      Zhang Z., Henzel W.J.
      Protein Sci. 13:2819-2824(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 20-34.
    7. Cited for: FUNCTION, TISSUE SPECIFICITY.
    8. "Structure of C3b in complex with CRIg gives insights into regulation of complement activation."
      Wiesmann C., Katschke K.J., Yin J., Helmy K.Y., Steffek M., Fairbrother W.J., McCallum S.A., Embuscado L., DeForge L., Hass P.E., van Lookeren Campagne M.
      Nature 444:217-220(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS) OF 19-137 IN COMPLEX WITH C3B AND C3C, FUNCTION, DISULFIDE BOND.

    Entry informationi

    Entry nameiVSIG4_HUMAN
    AccessioniPrimary (citable) accession number: Q9Y279
    Secondary accession number(s): Q6UXI4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 15, 2005
    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

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Human chromosome X
      Human chromosome X: 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    6. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3