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Q62178

- SEM4A_MOUSE

UniProt

Q62178 - SEM4A_MOUSE

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Protein

Semaphorin-4A

Gene

Sema4a

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Adaptive immunity, Angiogenesis, Differentiation, Immunity, Neurogenesis

Enzyme and pathway databases

ReactomeiREACT_231928. Other semaphorin interactions.

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini33 – 682650ExtracellularSequence AnalysisAdd
BLAST
Transmembranei683 – 70321HelicalSequence AnalysisAdd
BLAST
Topological domaini704 – 76057CytoplasmicSequence AnalysisAdd
BLAST

GO - Cellular componenti

  1. integral component of membrane Source: UniProtKB-KW
  2. plasma membrane Source: UniProtKB-KW
Complete GO annotation...

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

BgeeiQ62178.
ExpressionAtlasiQ62178. baseline and differential.
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...

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.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000116087.
HOVERGENiHBG061165.
InParanoidiQ62178.
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

        10         20         30         40         50
MALPSLGQDS WSLLRVFFFQ LFLLPSLPPA SGTGGQGPMP RVKYHAGDGH
60 70 80 90 100
RALSFFQQKG LRDFDTLLLS DDGNTLYVGA REAVLALNIQ NPGIPRLKNM
110 120 130 140 150
IPWPASERKK TECAFKKKSN ETQCFNFIRV LVSYNATHLY ACGTFAFSPA
160 170 180 190 200
CTFIELQDSL LLPILIDKVM DGKGQSPFDP VHKHTAVLVD GMLYSGTMNN
210 220 230 240 250
FLGSEPILMR TLGSQPVLKT DIFLRWLHAD ASFVAAIPST QVVYFFFEET
260 270 280 290 300
ASEFDFFEEL YISRVAQVCK NDVGGEKLLQ KKWTTFLKAQ LLCAQPGQLP
310 320 330 340 350
FNIIRHAVLL PADSPSVSRI YAVFTSQWQV GGTRSSAVCA FSLTDIERVF
360 370 380 390 400
KGKYKELNKE TSRWTTYRGS EVSPRPGSCS MGPSSDKALT FMKDHFLMDE
410 420 430 440 450
HVVGTPLLVK SGVEYTRLAV ESARGLDGSS HVVMYLGTST GSLHKAVVPQ
460 470 480 490 500
DSSAYLVEEI QLSPDSEPVR NLQLAPAQGA VFAGFSGGIW RVPRANCSVY
510 520 530 540 550
ESCVDCVLAR DPHCAWDPES RLCSLLSGST KPWKQDMERG NPEWVCTRGP
560 570 580 590 600
MARSPRRQSP PQLIKEVLTV PNSILELPCP HLSALASYHW SHGRAKISEA
610 620 630 640 650
SATVYNGSLL LLPQDGVGGL YQCVATENGY SYPVVSYWVD SQDQPLALDP
660 670 680 690 700
ELAGVPRERV QVPLTRVGGG ASMAAQRSYW PHFLIVTVLL AIVLLGVLTL
710 720 730 740 750
LLASPLGALR ARGKVQGCGM LPPREKAPLS RDQHLQPSKD HRTSASDVDA
760
DNNHLGAEVA
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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 ENSGT00760000118854.
HOGENOMi HOG000116087.
HOVERGENi HBG061165.
InParanoidi Q62178.
KOi K06521.
OMAi FAFSPAC.
OrthoDBi EOG7H791Q.
PhylomeDBi Q62178.
TreeFami TF316102.

Enzyme and pathway databases

Reactomei REACT_231928. Other semaphorin interactions.

Miscellaneous databases

ChiTaRSi Sema4a. mouse.
NextBioi 298207.
PROi Q62178.
SOURCEi Search...

Gene expression databases

Bgeei Q62178.
ExpressionAtlasi Q62178. baseline and differential.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 120 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