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Q62178 (SEM4A_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 115. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Semaphorin-4A
Alternative name(s):
Semaphorin-B
Short name=Sema B
Gene names
Name:Sema4a
Synonyms:Semab, SemB
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length760 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.4 Ref.6 Ref.7 Ref.10

Subunit structure

Interacts with PLXNB1, PLXNB2, PLXNB3 and PLXND1. Probable ligand for TIMD2. Ref.4 Ref.7 Ref.10

Subcellular location

Cell membrane; Single-pass type I membrane protein Ref.4 Ref.6 Ref.7 Ref.10.

Developmental stage

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.

Disruption phenotype

Results are contradictory; one study (Ref.6) 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 (Ref.5) gene disruption leads to degeneration of photoreceptor cells in the retina within the first month of life. Ref.5 Ref.6 Ref.7

Sequence similarities

Belongs to the semaphorin family.

Contains 1 Ig-like C2-type (immunoglobulin-like) domain.

Contains 1 PSI domain.

Contains 1 Sema domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 3232 Potential
Chain33 – 760728Semaphorin-4A
PRO_0000032323

Regions

Topological domain33 – 682650Extracellular Potential
Transmembrane683 – 70321Helical; Potential
Topological domain704 – 76057Cytoplasmic Potential
Domain36 – 494459Sema
Domain496 – 54752PSI
Domain572 – 63059Ig-like C2-type
Compositional bias609 – 6124Poly-Leu

Amino acid modifications

Glycosylation1201N-linked (GlcNAc...) Potential
Glycosylation1351N-linked (GlcNAc...) Potential
Glycosylation4961N-linked (GlcNAc...) Potential
Glycosylation6061N-linked (GlcNAc...) Potential
Disulfide bond113 ↔ 124 By similarity
Disulfide bond142 ↔ 151 By similarity
Disulfide bond269 ↔ 379 By similarity
Disulfide bond293 ↔ 339 By similarity
Disulfide bond497 ↔ 514 By similarity
Disulfide bond506 ↔ 523 By similarity
Disulfide bond579 ↔ 623 By similarity

Experimental info

Sequence conflict831A → T in CAA59983. Ref.1
Sequence conflict178 – 1858FDPVHKHT → LTLFTSTQ in CAA59983. Ref.1
Sequence conflict2151Q → H in CAA59983. Ref.1
Sequence conflict4421S → P in CAA59983. Ref.1
Sequence conflict5781P → R in CAA59983. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Q62178 [UniParc].

Last modified July 27, 2011. Version 2.
Checksum: C13BD31BD90BE3D9

FASTA76083,421
        10         20         30         40         50         60 
MALPSLGQDS WSLLRVFFFQ LFLLPSLPPA SGTGGQGPMP RVKYHAGDGH RALSFFQQKG 

        70         80         90        100        110        120 
LRDFDTLLLS DDGNTLYVGA REAVLALNIQ NPGIPRLKNM IPWPASERKK TECAFKKKSN 

       130        140        150        160        170        180 
ETQCFNFIRV LVSYNATHLY ACGTFAFSPA CTFIELQDSL LLPILIDKVM DGKGQSPFDP 

       190        200        210        220        230        240 
VHKHTAVLVD GMLYSGTMNN FLGSEPILMR TLGSQPVLKT DIFLRWLHAD ASFVAAIPST 

       250        260        270        280        290        300 
QVVYFFFEET ASEFDFFEEL YISRVAQVCK NDVGGEKLLQ KKWTTFLKAQ LLCAQPGQLP 

       310        320        330        340        350        360 
FNIIRHAVLL PADSPSVSRI YAVFTSQWQV GGTRSSAVCA FSLTDIERVF KGKYKELNKE 

       370        380        390        400        410        420 
TSRWTTYRGS EVSPRPGSCS MGPSSDKALT FMKDHFLMDE HVVGTPLLVK SGVEYTRLAV 

       430        440        450        460        470        480 
ESARGLDGSS HVVMYLGTST GSLHKAVVPQ DSSAYLVEEI QLSPDSEPVR NLQLAPAQGA 

       490        500        510        520        530        540 
VFAGFSGGIW RVPRANCSVY ESCVDCVLAR DPHCAWDPES RLCSLLSGST KPWKQDMERG 

       550        560        570        580        590        600 
NPEWVCTRGP MARSPRRQSP PQLIKEVLTV PNSILELPCP HLSALASYHW SHGRAKISEA 

       610        620        630        640        650        660 
SATVYNGSLL LLPQDGVGGL YQCVATENGY SYPVVSYWVD SQDQPLALDP ELAGVPRERV 

       670        680        690        700        710        720 
QVPLTRVGGG ASMAAQRSYW PHFLIVTVLL AIVLLGVLTL LLASPLGALR ARGKVQGCGM 

       730        740        750        760 
LPPREKAPLS RDQHLQPSKD HRTSASDVDA DNNHLGAEVA 

« Hide

References

« Hide 'large scale' references
[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]"Lineage-specific biology revealed by a finished genome assembly of the mouse."
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. expand/collapse author list , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P.
PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract]
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]"Severe retinal degeneration associated with disruption of semaphorin 4A."
Rice D.S., Huang W., Jones H.A., Hansen G., Ye G.L., Xu N., Wilson E.A., Troughton K., Vaddi K., Newton R.C., Zambrowicz B.P., Sands A.T.
Invest. Ophthalmol. Vis. Sci. 45:2767-2777(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
[6]"Nonredundant roles of Sema4A in the immune system: defective T cell priming and Th1/Th2 regulation in Sema4A-deficient mice."
Kumanogoh A., Shikina T., Suzuki K., Uematsu S., Yukawa K., Kashiwamura S., Tsutsui H., Yamamoto M., Takamatsu H., Ko-Mitamura E.P., Takegahara N., Marukawa S., Ishida I., Morishita H., Prasad D.V., Tamura M., Mizui M., Toyofuku T. expand/collapse author list , Akira S., Takeda K., Okabe M., Kikutani H.
Immunity 22:305-316(2005) [PubMed] [Europe PMC] [Abstract]
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]"Large-scale phosphorylation analysis of mouse liver."
Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRI48745.
RefSeqNP_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.
UniGeneMm.439752.

3D structure databases

ProteinModelPortalQ62178.
SMRQ62178. Positions 37-627.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING10090.ENSMUSP00000029700.

PTM databases

PhosphoSiteQ62178.

Proteomic databases

PaxDbQ62178.
PRIDEQ62178.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000029700; ENSMUSP00000029700; ENSMUSG00000028064.
ENSMUST00000165898; ENSMUSP00000128510; ENSMUSG00000028064.
ENSMUST00000166237; ENSMUSP00000125909; ENSMUSG00000028064.
ENSMUST00000169222; ENSMUSP00000128887; ENSMUSG00000028064.
GeneID20351.
KEGGmmu:20351.
UCSCuc008pvg.2. mouse.

Organism-specific databases

CTD64218.
MGIMGI:107560. Sema4a.

Phylogenomic databases

eggNOGNOG287504.
GeneTreeENSGT00560000076864.
HOGENOMHOG000116087.
HOVERGENHBG061165.
KOK06521.
OMAFAFSPAC.
OrthoDBEOG7H791Q.
PhylomeDBQ62178.
TreeFamTF316102.

Gene expression databases

ArrayExpressQ62178.
BgeeQ62178.
GenevestigatorQ62178.

Family and domain databases

Gene3D2.130.10.10. 1 hit.
InterProIPR016201. Plexin-like_fold.
IPR002165. Plexin_repeat.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERPTHR11036. PTHR11036. 1 hit.
PfamPF01437. PSI. 1 hit.
PF01403. Sema. 1 hit.
[Graphical view]
SMARTSM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
PROSITEPS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSEMA4A. mouse.
NextBio298207.
PROQ62178.
SOURCESearch...

Entry information

Entry nameSEM4A_MOUSE
AccessionPrimary (citable) accession number: Q62178
Secondary accession number(s): D3Z5L2
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: July 27, 2011
Last modified: April 16, 2014
This is version 115 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot