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Q9Y279

- VSIG4_HUMAN

UniProt

Q9Y279 - VSIG4_HUMAN

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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

Functioni

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

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
Complete GO annotation...

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini20 – 283264ExtracellularSequence AnalysisAdd
BLAST
Transmembranei284 – 30421HelicalSequence AnalysisAdd
BLAST
Topological domaini305 – 39995CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

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

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

BgeeiQ9Y279.
CleanExiHS_VSIG4.
GenevestigatoriQ9Y279.

Organism-specific databases

HPAiCAB026000.
HPA003903.

Interactioni

Binary interactionsi

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

Protein-protein interaction databases

BioGridi116455. 60 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 – 326Combined sources
Beta strandi37 – 393Combined sources
Beta strandi50 – 589Combined sources
Beta strandi60 – 634Combined sources
Beta strandi65 – 717Combined sources
Beta strandi74 – 774Combined sources
Helixi80 – 823Combined sources
Turni83 – 853Combined sources
Beta strandi86 – 883Combined sources
Beta strandi98 – 1003Combined sources
Helixi105 – 1073Combined sources
Beta strandi109 – 11810Combined sources
Beta strandi124 – 13613Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.

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.
GeneTreeiENSGT00390000001432.
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

        10         20         30         40         50
MGILLGLLLL GHLTVDTYGR PILEVPESVT GPWKGDVNLP CTYDPLQGYT
60 70 80 90 100
QVLVKWLVQR GSDPVTIFLR DSSGDHIQQA KYQGRLHVSH KVPGDVSLQL
110 120 130 140 150
STLEMDDRSH YTCEVTWQTP DGNQVVRDKI TELRVQKLSV SKPTVTTGSG
160 170 180 190 200
YGFTVPQGMR ISLQCQARGS PPISYIWYKQ QTNNQEPIKV ATLSTLLFKP
210 220 230 240 250
AVIADSGSYF CTAKGQVGSE QHSDIVKFVV KDSSKLLKTK TEAPTTMTYP
260 270 280 290 300
LKATSTVKQS WDWTTDMDGY LGETSAGPGK SLPVFAIILI ISLCCMVVFT
310 320 330 340 350
MAYIMLCRKT SQQEHVYEAA RAHAREANDS GETMRVAIFA SGCSSDEPTS
360 370 380 390
QNLGNNYSDE PCIGQEYQII AQINGNYARL LDTVPLDYEF LATEGKSVC
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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. 60 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.
GeneTreei ENSGT00390000001432.
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

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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 125 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