Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

Q9Y279 (VSIG4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 117. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
V-set and immunoglobulin domain-containing protein 4
Alternative name(s):
Protein Z39Ig
Gene names
Name:VSIG4
Synonyms:CRIg, Z39IG
ORF Names:UNQ317/PRO362
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length399 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Phagocytic receptor, strong negative regulator of T-cell proliferation and IL2 production. Potent inhibitor of the alternative complement pathway convertases. Ref.7 Ref.8

Subcellular location

Membrane; Single-pass type I membrane protein Probable.

Tissue specificity

Abundantly expressed in several fetal tissues. In adult tissues, highest expression in lung and placenta. Expressed in resting macrophages. Ref.1 Ref.7

Sequence similarities

Contains 2 Ig-like (immunoglobulin-like) domains.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

C3P010245EBI-903144,EBI-905851

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9Y279-1)

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.
Isoform 2 (identifier: Q9Y279-2)

The sequence of this isoform differs from the canonical sequence as follows:
     322-399: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q9Y279-3)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1919 Ref.6
Chain20 – 399380V-set and immunoglobulin domain-containing protein 4
PRO_0000015006

Regions

Topological domain20 – 283264Extracellular Potential
Transmembrane284 – 30421Helical; Potential
Topological domain305 – 39995Cytoplasmic Potential
Domain21 – 131111Ig-like 1
Domain143 – 22684Ig-like 2

Amino acid modifications

Disulfide bond41 ↔ 113 Ref.8
Disulfide bond165 ↔ 211 By similarity

Natural variations

Alternative sequence138 – 23295LSVSK…FVVKD → H in isoform 3.
VSP_041213
Alternative sequence322 – 39978Missing in isoform 2.
VSP_012813
Natural variant1081R → W.
Corresponds to variant rs34581041 [ dbSNP | Ensembl ].
VAR_049956
Natural variant2721G → E.
Corresponds to variant rs34222730 [ dbSNP | Ensembl ].
VAR_049957
Natural variant2791G → E.
Corresponds to variant rs17315645 [ dbSNP | Ensembl ].
VAR_049958
Natural variant3971S → I.
Corresponds to variant rs35553694 [ dbSNP | Ensembl ].
VAR_049959

Secondary structure

......................... 399
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 1, 1999. Version 1.
Checksum: 735CA3BC58185035

FASTA39943,987
        10         20         30         40         50         60 
MGILLGLLLL GHLTVDTYGR PILEVPESVT GPWKGDVNLP CTYDPLQGYT QVLVKWLVQR 

        70         80         90        100        110        120 
GSDPVTIFLR DSSGDHIQQA KYQGRLHVSH KVPGDVSLQL STLEMDDRSH YTCEVTWQTP 

       130        140        150        160        170        180 
DGNQVVRDKI TELRVQKLSV SKPTVTTGSG YGFTVPQGMR ISLQCQARGS PPISYIWYKQ 

       190        200        210        220        230        240 
QTNNQEPIKV ATLSTLLFKP AVIADSGSYF CTAKGQVGSE QHSDIVKFVV KDSSKLLKTK 

       250        260        270        280        290        300 
TEAPTTMTYP LKATSTVKQS WDWTTDMDGY LGETSAGPGK SLPVFAIILI ISLCCMVVFT 

       310        320        330        340        350        360 
MAYIMLCRKT SQQEHVYEAA RAHAREANDS GETMRVAIFA SGCSSDEPTS QNLGNNYSDE 

       370        380        390 
PCIGQEYQII AQINGNYARL LDTVPLDYEF LATEGKSVC 

« Hide

Isoform 2 [UniParc].

Checksum: B2AB2E3151D39C6E
Show »

FASTA32135,544
Isoform 3 [UniParc].

Checksum: 12C57C74CCD69134
Show »

FASTA30533,857

References

« Hide 'large scale' references
[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]"The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment."
Clark H.F., Gurney A.L., Abaya E., Baker K., Baldwin D.T., Brush J., Chen J., Chow B., Chui C., Crowley C., Currell B., Deuel B., Dowd P., Eaton D., Foster J.S., Grimaldi C., Gu Q., Hass P.E. expand/collapse author list , Heldens S., Huang A., Kim H.S., Klimowski L., Jin Y., Johnson S., Lee J., Lewis L., Liao D., Mark M.R., Robbie E., Sanchez C., Schoenfeld J., Seshagiri S., Simmons L., Singh J., Smith V., Stinson J., Vagts A., Vandlen R.L., Watanabe C., Wieand D., Woods K., Xie M.-H., Yansura D.G., Yi S., Yu G., Yuan J., Zhang M., Zhang Z., Goddard A.D., Wood W.I., Godowski P.J., Gray A.M.
Genome Res. 13:2265-2270(2003) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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]"VSIG4, a B7 family-related protein, is a negative regulator of T cell activation."
Vogt L., Schmitz N., Kurrer M.O., Bauer M., Hinton H.I., Behnke S., Gatto D., Sebbel P., Beerli R.R., Sonderegger I., Kopf M., Saudan P., Bachmann M.F.
J. Clin. Invest. 116:2817-2826(2006) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_001093901.1. NM_001100431.1.
NP_001171759.1. NM_001184830.1.
NP_001171760.1. NM_001184831.1.
NP_001244332.1. NM_001257403.1.
NP_009199.1. NM_007268.2.
UniGeneHs.8904.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2ICCX-ray1.20A19-137[»]
2ICEX-ray3.10S/T19-137[»]
2ICFX-ray4.10S19-137[»]
ProteinModelPortalQ9Y279.
SMRQ9Y279. Positions 19-236.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116455. 3 interactions.
IntActQ9Y279. 2 interactions.
STRING9606.ENSP00000363869.

PTM databases

PhosphoSiteQ9Y279.

Polymorphism databases

DMDM59799152.

Proteomic databases

PaxDbQ9Y279.
PRIDEQ9Y279.

Protocols and materials databases

DNASU11326.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000374737; ENSP00000363869; ENSG00000155659. [Q9Y279-1]
ENST00000412866; ENSP00000394143; ENSG00000155659. [Q9Y279-3]
ENST00000455586; ENSP00000411581; ENSG00000155659. [Q9Y279-2]
GeneID11326.
KEGGhsa:11326.
UCSCuc004dwh.2. human. [Q9Y279-1]
uc004dwi.2. human. [Q9Y279-3]

Organism-specific databases

CTD11326.
GeneCardsGC0XM065241.
HGNCHGNC:17032. VSIG4.
HPACAB026000.
HPA003903.
MIM300353. gene.
neXtProtNX_Q9Y279.
PharmGKBPA134986421.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG39012.
HOGENOMHOG000137602.
HOVERGENHBG055008.
InParanoidQ9Y279.
OMAYGHPILE.
TreeFamTF336175.

Gene expression databases

ArrayExpressQ9Y279.
BgeeQ9Y279.
CleanExHS_VSIG4.
GenevestigatorQ9Y279.

Family and domain databases

Gene3D2.60.40.10. 2 hits.
InterProIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR003598. Ig_sub2.
IPR013106. Ig_V-set.
[Graphical view]
PfamPF07686. V-set. 1 hit.
[Graphical view]
SMARTSM00409. IG. 1 hit.
SM00408. IGc2. 1 hit.
[Graphical view]
PROSITEPS50835. IG_LIKE. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9Y279.
GenomeRNAi11326.
NextBio43025.
PROQ9Y279.
SOURCESearch...

Entry information

Entry nameVSIG4_HUMAN
AccessionPrimary (citable) accession number: Q9Y279
Secondary accession number(s): Q6UXI4
Entry history
Integrated into UniProtKB/Swiss-Prot: February 15, 2005
Last sequence update: November 1, 1999
Last modified: March 19, 2014
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome X

Human chromosome X: entries, gene names and cross-references to MIM