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Protein

Semaphorin-4D

Gene

Sema4d

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

Functioni

Cell surface receptor for PLXN1B and PLXNB2 that plays an important role in cell-cell signaling. Promotes reorganization of the actin cytoskeleton and plays a role in axonal growth cone guidance in the developing central nervous system. Regulates dendrite and axon branching and morphogenesis. Promotes the migration of cerebellar granule cells and of endothelial cells. Plays a role in the immune system; induces B-cells to aggregate and improves their viability (in vitro). Promotes signaling via SRC and PTK2B/PYK2, which then mediates activation of phosphatidylinositol 3-kinase and of the AKT1 signaling cascade. Interaction with PLXNB1 mediates activation of RHOA (By similarity).By similarity1 Publication

GO - Molecular functioni

  • receptor activity Source: MGI
  • receptor binding Source: MGI
  • semaphorin receptor binding Source: BHF-UCL
  • transmembrane signaling receptor activity Source: UniProtKB

GO - Biological processi

  • leukocyte aggregation Source: UniProtKB
  • negative chemotaxis Source: GO_Central
  • negative regulation of alkaline phosphatase activity Source: BHF-UCL
  • negative regulation of cell adhesion Source: UniProtKB
  • negative regulation of osteoblast differentiation Source: BHF-UCL
  • negative regulation of peptidyl-tyrosine phosphorylation Source: BHF-UCL
  • negative regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  • ossification involved in bone maturation Source: BHF-UCL
  • positive regulation of axonogenesis Source: MGI
  • positive regulation of cell migration Source: BHF-UCL
  • positive regulation of collateral sprouting Source: UniProtKB
  • positive regulation of GTPase activity Source: BHF-UCL
  • positive regulation of peptidyl-tyrosine phosphorylation Source: BHF-UCL
  • positive regulation of phosphatidylinositol 3-kinase signaling Source: UniProtKB
  • positive regulation of protein phosphorylation Source: UniProtKB
  • regulation of cell projection organization Source: UniProtKB
  • regulation of cell shape Source: UniProtKB
  • regulation of dendrite morphogenesis Source: UniProtKB
  • semaphorin-plexin signaling pathway Source: UniProtKB
  • semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis Source: BHF-UCL

Keywordsi

Molecular functionDevelopmental protein
Biological processDifferentiation, Neurogenesis

Enzyme and pathway databases

ReactomeiR-MMU-416550. Sema4D mediated inhibition of cell attachment and migration.
R-MMU-416572. Sema4D induced cell migration and growth-cone collapse.
R-MMU-416700. Other semaphorin interactions.

Names & Taxonomyi

Protein namesi
Recommended name:
Semaphorin-4D
Alternative name(s):
M-Sema G
Semaphorin-C-like 2
Semaphorin-J
Short name:
Sema J
CD_antigen: CD100
Gene namesi
Name:Sema4d
Synonyms:Semacl2, Semaj
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:109244. Sema4d.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini24 – 733ExtracellularSequence analysisAdd BLAST710
Transmembranei734 – 754HelicalSequence analysisAdd BLAST21
Topological domaini755 – 861CytoplasmicSequence analysisAdd BLAST107

GO - Cellular componenti

  • extracellular space Source: BHF-UCL
  • integral component of plasma membrane Source: MGI
  • membrane Source: BHF-UCL
  • plasma membrane Source: GO_Central

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 23Sequence analysisAdd BLAST23
ChainiPRO_000003232824 – 861Semaphorin-4DAdd BLAST838

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi49N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi77N-linked (GlcNAc...) asparagine1 Publication1
Disulfide bondi97 ↔ 108By similarity
Disulfide bondi126 ↔ 135By similarity
Glycosylationi139N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi191N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi257 ↔ 370By similarity
Disulfide bondi281 ↔ 326By similarity
Glycosylationi379N-linked (GlcNAc...) asparagine1 Publication1
Glycosylationi419N-linked (GlcNAc...) asparagine1 Publication1
Disulfide bondi503 ↔ 520By similarity
Disulfide bondi509 ↔ 553By similarity
Disulfide bondi512 ↔ 529By similarity
Disulfide bondi576 ↔ 624By similarity
Glycosylationi613N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi632N-linked (GlcNAc...) asparagineSequence analysis1
Modified residuei782PhosphoserineCombined sources1
Modified residuei832PhosphoserineBy similarity1

Keywords - PTMi

Disulfide bond, Glycoprotein, Phosphoprotein

Proteomic databases

EPDiO09126.
MaxQBiO09126.
PaxDbiO09126.
PeptideAtlasiO09126.
PRIDEiO09126.

PTM databases

iPTMnetiO09126.
PhosphoSitePlusiO09126.
SwissPalmiO09126.

Expressioni

Tissue specificityi

Strongly expressed in lymphoid tissues, especially in the thymus, as well as in the nervous tissues.

Gene expression databases

BgeeiENSMUSG00000021451.
GenevisibleiO09126. MM.

Interactioni

Subunit structurei

Homodimer. Binds PLXNB1 (By similarity). Interacts with PLXNB2.By similarity1 Publication

GO - Molecular functioni

  • receptor binding Source: MGI
  • semaphorin receptor binding Source: BHF-UCL

Protein-protein interaction databases

IntActiO09126. 1 interactor.
MINTiMINT-4996140.
STRINGi10090.ENSMUSP00000021900.

Structurei

3D structure databases

ProteinModelPortaliO09126.
SMRiO09126.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini24 – 500SemaPROSITE-ProRule annotationAdd BLAST477
Domaini502 – 551PSIAdd BLAST50
Domaini555 – 636Ig-like C2-typeAdd BLAST82

Sequence similaritiesi

Belongs to the semaphorin family.Curated

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3611. Eukaryota.
ENOG410XQZC. LUCA.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000116087.
HOVERGENiHBG061627.
InParanoidiO09126.
KOiK06521.
OMAiFCQATGP.
OrthoDBiEOG091G01W0.
TreeFamiTF316102.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProiView protein in InterPro
IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003598. Ig_sub2.
IPR013151. Immunoglobulin.
IPR002165. Plexin_repeat.
IPR016201. PSI.
IPR001627. Semap_dom.
IPR027231. Semaphorin.
IPR015943. WD40/YVTN_repeat-like_dom.
PANTHERiPTHR11036. PTHR11036. 1 hit.
PfamiView protein in Pfam
PF00047. ig. 1 hit.
PF01437. PSI. 1 hit.
PF01403. Sema. 1 hit.
SMARTiView protein in SMART
SM00408. IGc2. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
SUPFAMiSSF101912. SSF101912. 1 hit.
SSF48726. SSF48726. 1 hit.
PROSITEiView protein in PROSITE
PS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.

Sequencei

Sequence statusi: Complete.

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

O09126-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRMCAPVRGL FLALVVVLRT AVAFAPVPRL TWEHGEVGLV QFHKPGIFNY
60 70 80 90 100
SALLMSEDKD TLYVGAREAV FAVNALNISE KQHEVYWKVS EDKKSKCAEK
110 120 130 140 150
GKSKQTECLN YIRVLQPLSS TSLYVCGTNA FQPTCDHLNL TSFKFLGKSE
160 170 180 190 200
DGKGRCPFDP AHSYTSVMVG GELYSGTSYN FLGSEPIISR NSSHSPLRTE
210 220 230 240 250
YAIPWLNEPS FVFADVIQKS PDGPEGEDDK VYFFFTEVSV EYEFVFKLMI
260 270 280 290 300
PRVARVCKGD QGGLRTLQKK WTSFLKARLI CSKPDSGLVF NILQDVFVLR
310 320 330 340 350
APGLKEPVFY AVFTPQLNNV GLSAVCAYTL ATVEAVFSRG KYMQSATVEQ
360 370 380 390 400
SHTKWVRYNG PVPTPRPGAC IDSEARAANY TSSLNLPDKT LQFVKDHPLM
410 420 430 440 450
DDSVTPIDNR PKLIKKDVNY TQIVVDRTQA LDGTFYDVMF ISTDRGALHK
460 470 480 490 500
AVILTKEVHV IEETQLFRDS EPVLTLLLSS KKGRKFVYAG SNSGVVQAPL
510 520 530 540 550
AFCEKHGSCE DCVLARDPYC AWSPAIKACV TLHQEEASSR GWIQDMSGDT
560 570 580 590 600
SSCLDKSKES FNQHFFKHGG TAELKCFQKS NLARVVWKFQ NGELKAASPK
610 620 630 640 650
YGFVGRKHLL IFNLSDGDSG VYQCLSEERV RNKTVSQLLA KHVLEVKMVP
660 670 680 690 700
RTPPSPTSED AQTEGSKITS KMPVASTQGS SPPTPALWAT SPRAATLPPK
710 720 730 740 750
SSSGTSCEPK MVINTVPQLH SEKTVYLKSS DNRLLMSLLL FIFVLFLCLF
760 770 780 790 800
SYNCYKGYLP GQCLKFRSAL LLGKKTPKSD FSDLEQSVKE TLVEPGSFSQ
810 820 830 840 850
QNGDHPKPAL DTGYETEQDT ITSKVPTDRE DSQRIDELSA RDKPFDVKCE
860
LKFADSDADG D
Length:861
Mass (Da):95,640
Last modified:July 27, 2011 - v2
Checksum:iB962D4E4CF37FFD9
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti470S → F in AAC52964 (PubMed:8969198).Curated1
Sequence conflicti661A → V in AAC52964 (PubMed:8969198).Curated1
Sequence conflicti675A → G in AAC52964 (PubMed:8969198).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U69535 mRNA. Translation: AAC52964.1.
CH466546 Genomic DNA. Translation: EDL41105.1.
CH466546 Genomic DNA. Translation: EDL41106.1.
CH466546 Genomic DNA. Translation: EDL41107.1.
BC049780 mRNA. Translation: AAH49780.2.
CCDSiCCDS26514.1.
RefSeqiNP_001268809.1. NM_001281880.1.
NP_038688.2. NM_013660.4.
UniGeneiMm.33903.

Genome annotation databases

EnsembliENSMUST00000021900; ENSMUSP00000021900; ENSMUSG00000021451.
ENSMUST00000110039; ENSMUSP00000105666; ENSMUSG00000021451.
ENSMUST00000110040; ENSMUSP00000105667; ENSMUSG00000021451.
GeneIDi20354.
KEGGimmu:20354.
UCSCiuc007qmn.2. mouse.

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.

Entry informationi

Entry nameiSEM4D_MOUSE
AccessioniPrimary (citable) accession number: O09126
Secondary accession number(s): Q6GTM9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: July 27, 2011
Last modified: July 5, 2017
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. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families