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Protein

Semaphorin-4A

Gene

Sema4a

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

  • chemorepellent activity Source: GO_Central
  • neuropilin binding Source: GO_Central
  • semaphorin receptor binding Source: GO_Central

GO - Biological processi

Keywordsi

Molecular functionDevelopmental protein
Biological processAdaptive 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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:107560 Sema4a

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

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

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...) asparagineSequence analysis1
Glycosylationi135N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi142 ↔ 151PROSITE-ProRule annotation
Disulfide bondi269 ↔ 379PROSITE-ProRule annotation
Disulfide bondi293 ↔ 339PROSITE-ProRule annotation
Glycosylationi496N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi497 ↔ 514PROSITE-ProRule annotation
Disulfide bondi506 ↔ 523PROSITE-ProRule annotation
Disulfide bondi579 ↔ 623PROSITE-ProRule annotation
Glycosylationi606N-linked (GlcNAc...) asparagineSequence analysis1

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

EPDiQ62178
MaxQBiQ62178
PaxDbiQ62178
PeptideAtlasiQ62178
PRIDEiQ62178

PTM databases

iPTMnetiQ62178
PhosphoSitePlusiQ62178
SwissPalmiQ62178

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 Expressed in 284 organ(s), highest expression level in epithelium of small intestine
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

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

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

Family and domain databases

Gene3Di2.130.10.10, 1 hit
2.60.40.10, 1 hit
InterProiView protein in InterPro
IPR013783 Ig-like_fold
IPR002165 Plexin_repeat
IPR016201 PSI
IPR001627 Semap_dom
IPR036352 Semap_dom_sf
IPR027231 Semaphorin
IPR015943 WD40/YVTN_repeat-like_dom_sf
PANTHERiPTHR11036 PTHR11036, 1 hit
PfamiView protein in Pfam
PF01437 PSI, 1 hit
PF01403 Sema, 1 hit
SMARTiView protein in SMART
SM00423 PSI, 1 hit
SM00630 Sema, 1 hit
SUPFAMiSSF101912 SSF101912, 1 hit
PROSITEiView protein in PROSITE
PS51004 SEMA, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry has 1 described isoform and 9 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 9 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
D3YWV5D3YWV5_MOUSE
Semaphorin-4A
Sema4a
628Annotation score:
D3YUM4D3YUM4_MOUSE
Semaphorin-4A
Sema4a
203Annotation score:
D3Z336D3Z336_MOUSE
Semaphorin-4A
Sema4a
113Annotation score:
D3YZ30D3YZ30_MOUSE
Semaphorin-4A
Sema4a
233Annotation score:
V9GXF5V9GXF5_MOUSE
Semaphorin-4A
Sema4a
170Annotation score:
V9GXH9V9GXH9_MOUSE
Semaphorin-4A
Sema4a
180Annotation score:
D3YVM6D3YVM6_MOUSE
Semaphorin-4A
Sema4a
60Annotation score:
V9GWW2V9GWW2_MOUSE
Semaphorin-4A
Sema4a
47Annotation score:
D3YWK5D3YWK5_MOUSE
Semaphorin-4A
Sema4a
17Annotation score:

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

Similar proteinsi

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
SwissPalmiQ62178

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
OMAiSQWQIGG
OrthoDBiEOG091G01W0
PhylomeDBiQ62178
TreeFamiTF316102

Enzyme and pathway databases

ReactomeiR-MMU-416700 Other semaphorin interactions

Miscellaneous databases

ChiTaRSiSema4a mouse
PROiPR:Q62178
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000028064 Expressed in 284 organ(s), highest expression level in epithelium of small intestine
ExpressionAtlasiQ62178 baseline and differential
GenevisibleiQ62178 MM

Family and domain databases

Gene3Di2.130.10.10, 1 hit
2.60.40.10, 1 hit
InterProiView protein in InterPro
IPR013783 Ig-like_fold
IPR002165 Plexin_repeat
IPR016201 PSI
IPR001627 Semap_dom
IPR036352 Semap_dom_sf
IPR027231 Semaphorin
IPR015943 WD40/YVTN_repeat-like_dom_sf
PANTHERiPTHR11036 PTHR11036, 1 hit
PfamiView protein in Pfam
PF01437 PSI, 1 hit
PF01403 Sema, 1 hit
SMARTiView protein in SMART
SM00423 PSI, 1 hit
SM00630 Sema, 1 hit
SUPFAMiSSF101912 SSF101912, 1 hit
PROSITEiView protein in PROSITE
PS51004 SEMA, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSEM4A_MOUSE
AccessioniPrimary (citable) accession number: Q62178
Secondary accession number(s): D3Z5L2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: July 27, 2011
Last modified: November 7, 2018
This is version 150 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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