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Protein

Semaphorin-4A

Gene

Sema4a

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: 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

GO - Biological processi

  • angiogenesis Source: UniProtKB-KW
  • axonogenesis Source: UniProtKB
  • negative chemotaxis Source: GO_Central
  • negative regulation of angiogenesis Source: UniProtKB
  • negative regulation of axon extension involved in axon guidance Source: GO_Central
  • neural crest cell migration Source: GO_Central
  • positive regulation of cell migration Source: GO_Central
  • regulation of cell shape Source: UniProtKB
  • regulation of endothelial cell migration Source: UniProtKB
  • semaphorin-plexin signaling pathway Source: UniProtKB
  • T cell differentiation involved in immune response Source: UniProtKB
  • 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

ReactomeiR-MMU-416700. 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
Proteomesi
  • UP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:107560. Sema4a.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini33 – 682ExtracellularSequence analysisAdd BLAST650
Transmembranei683 – 703HelicalSequence analysisAdd BLAST21
Topological domaini704 – 760CytoplasmicSequence analysisAdd BLAST57

GO - Cellular componenti

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)DescriptionActionsGraphical viewLength
Signal peptidei1 – 32Sequence analysisAdd BLAST32
ChainiPRO_000003232333 – 760Semaphorin-4AAdd BLAST728

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi113 ↔ 124PROSITE-ProRule annotation
Glycosylationi120N-linked (GlcNAc...)Sequence analysis1
Glycosylationi135N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi142 ↔ 151PROSITE-ProRule annotation
Disulfide bondi269 ↔ 379PROSITE-ProRule annotation
Disulfide bondi293 ↔ 339PROSITE-ProRule annotation
Glycosylationi496N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi497 ↔ 514PROSITE-ProRule annotation
Disulfide bondi506 ↔ 523PROSITE-ProRule annotation
Disulfide bondi579 ↔ 623PROSITE-ProRule annotation
Glycosylationi606N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

EPDiQ62178.
MaxQBiQ62178.
PaxDbiQ62178.
PeptideAtlasiQ62178.
PRIDEiQ62178.

PTM databases

iPTMnetiQ62178.
PhosphoSitePlusiQ62178.

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

BgeeiENSMUSG00000028064.
ExpressionAtlasiQ62178. baseline and differential.
GenevisibleiQ62178. MM.

Interactioni

Subunit structurei

Interacts with PLXNB1, PLXNB2, PLXNB3 and PLXND1. Probable ligand for TIMD2.3 Publications

GO - Molecular functioni

Protein-protein interaction databases

BioGridi203166. 5 interactors.
STRINGi10090.ENSMUSP00000029700.

Structurei

3D structure databases

ProteinModelPortaliQ62178.
SMRiQ62178.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini36 – 494SemaPROSITE-ProRule annotationAdd BLAST459
Domaini496 – 547PSIAdd BLAST52
Domaini572 – 630Ig-like C2-typeAdd BLAST59

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi609 – 612Poly-Leu4

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

eggNOGiKOG3611. Eukaryota.
ENOG410XQZC. LUCA.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000116087.
HOVERGENiHBG061165.
InParanoidiQ62178.
KOiK06521.
OMAiFAFSPAC.
OrthoDBiEOG091G01W0.
PhylomeDBiQ62178.
TreeFamiTF316102.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR002165. Plexin_repeat.
IPR016201. PSI.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 2 hits.
PfamiPF01437. PSI. 1 hit.
PF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 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)DescriptionActionsGraphical viewLength
Sequence conflicti83A → T in CAA59983 (PubMed:7748561).Curated1
Sequence conflicti178 – 185FDPVHKHT → LTLFTSTQ in CAA59983 (PubMed:7748561).Curated8
Sequence conflicti215Q → H in CAA59983 (PubMed:7748561).Curated1
Sequence conflicti442S → P in CAA59983 (PubMed:7748561).Curated1
Sequence conflicti578P → R in CAA59983 (PubMed:7748561).Curated1

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.
XP_011238353.1. XM_011240051.1.
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.
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.
XP_011238353.1. XM_011240051.1.
UniGeneiMm.439752.

3D structure databases

ProteinModelPortaliQ62178.
SMRiQ62178.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi203166. 5 interactors.
STRINGi10090.ENSMUSP00000029700.

PTM databases

iPTMnetiQ62178.
PhosphoSitePlusiQ62178.

Proteomic databases

EPDiQ62178.
MaxQBiQ62178.
PaxDbiQ62178.
PeptideAtlasiQ62178.
PRIDEiQ62178.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000029700; ENSMUSP00000029700; ENSMUSG00000028064.
ENSMUST00000165898; ENSMUSP00000128510; ENSMUSG00000028064.
ENSMUST00000166237; ENSMUSP00000125909; ENSMUSG00000028064.
ENSMUST00000169222; ENSMUSP00000128887; ENSMUSG00000028064.
GeneIDi20351.
KEGGimmu:20351.
UCSCiuc008pvg.2. mouse.

Organism-specific databases

CTDi64218.
MGIiMGI:107560. Sema4a.

Phylogenomic databases

eggNOGiKOG3611. Eukaryota.
ENOG410XQZC. LUCA.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000116087.
HOVERGENiHBG061165.
InParanoidiQ62178.
KOiK06521.
OMAiFAFSPAC.
OrthoDBiEOG091G01W0.
PhylomeDBiQ62178.
TreeFamiTF316102.

Enzyme and pathway databases

ReactomeiR-MMU-416700. Other semaphorin interactions.

Miscellaneous databases

ChiTaRSiSema4a. mouse.
PROiQ62178.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000028064.
ExpressionAtlasiQ62178. baseline and differential.
GenevisibleiQ62178. MM.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
InterProiIPR002165. Plexin_repeat.
IPR016201. PSI.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
[Graphical view]
PANTHERiPTHR11036. PTHR11036. 2 hits.
PfamiPF01437. PSI. 1 hit.
PF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
PROSITEiPS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetiSearch...

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 30, 2016
This is version 137 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.