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O09126 (SEM4D_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 123. 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-4D
Alternative name(s):
M-Sema G
Semaphorin-C-like 2
Semaphorin-J
Short name=Sema J
CD_antigen=CD100
Gene names
Name:Sema4d
Synonyms:Semacl2, Semaj
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length861 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 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. Ref.4

Subunit structure

Homodimer. Binds PLXNB1 By similarity. Interacts with PLXNB2. Ref.4

Subcellular location

Cell membrane; Single-pass type I membrane protein.

Tissue specificity

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

Sequence similarities

Belongs to the semaphorin family.

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

Contains 1 PSI domain.

Contains 1 Sema domain.

Ontologies

Keywords
   Biological processDifferentiation
Neurogenesis
   Cellular componentCell membrane
Membrane
   DomainImmunoglobulin domain
Signal
Transmembrane
Transmembrane helix
   Molecular functionDevelopmental protein
   PTMDisulfide bond
Glycoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processleukocyte aggregation

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of alkaline phosphatase activity

Inferred from direct assay PubMed 22019888. Source: BHF-UCL

negative regulation of cell adhesion

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of osteoblast differentiation

Inferred from mutant phenotype PubMed 22019888. Source: BHF-UCL

negative regulation of peptidyl-tyrosine phosphorylation

Inferred from direct assay PubMed 22019888. Source: BHF-UCL

negative regulation of transcription from RNA polymerase II promoter

Inferred from direct assay PubMed 22019888. Source: BHF-UCL

ossification involved in bone maturation

Inferred from mutant phenotype PubMed 22019888. Source: BHF-UCL

positive regulation of Rho GTPase activity

Inferred from mutant phenotype PubMed 22019888. Source: BHF-UCL

positive regulation of axonogenesis

Inferred from direct assay PubMed 15330859. Source: MGI

positive regulation of cell migration

Inferred from direct assay PubMed 22019888. Source: BHF-UCL

positive regulation of collateral sprouting

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of peptidyl-tyrosine phosphorylation

Inferred from direct assay PubMed 22019888. Source: BHF-UCL

positive regulation of phosphatidylinositol 3-kinase signaling

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of protein phosphorylation

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of cell projection organization

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of cell shape

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of dendrite morphogenesis

Inferred from sequence or structural similarity. Source: UniProtKB

semaphorin-plexin signaling pathway

Inferred from sequence or structural similarity. Source: UniProtKB

semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis

Inferred from mutant phenotype PubMed 22019888. Source: BHF-UCL

   Cellular_componentextracellular space

Inferred from direct assay PubMed 22019888. Source: BHF-UCL

integral component of plasma membrane

Inferred from electronic annotation. Source: Ensembl

membrane

Traceable author statement PubMed 22019888. Source: BHF-UCL

   Molecular_functionreceptor binding

Inferred from physical interaction PubMed 15330859. Source: MGI

semaphorin receptor binding

Inferred from physical interaction PubMed 22019888. Source: BHF-UCL

transmembrane signaling receptor activity

Inferred from sequence or structural similarity. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2323 Potential
Chain24 – 861838Semaphorin-4D
PRO_0000032328

Regions

Topological domain24 – 733710Extracellular Potential
Transmembrane734 – 75421Helical; Potential
Topological domain755 – 861107Cytoplasmic Potential
Domain24 – 500477Sema
Domain502 – 55150PSI
Domain555 – 63682Ig-like C2-type

Amino acid modifications

Glycosylation491N-linked (GlcNAc...) Potential
Glycosylation771N-linked (GlcNAc...) Ref.5
Glycosylation1391N-linked (GlcNAc...) Potential
Glycosylation1911N-linked (GlcNAc...) Potential
Glycosylation3791N-linked (GlcNAc...) Ref.5
Glycosylation4191N-linked (GlcNAc...) Ref.5
Glycosylation6131N-linked (GlcNAc...) Potential
Glycosylation6321N-linked (GlcNAc...) Potential
Disulfide bond97 ↔ 108 By similarity
Disulfide bond126 ↔ 135 By similarity
Disulfide bond257 ↔ 370 By similarity
Disulfide bond281 ↔ 326 By similarity
Disulfide bond503 ↔ 520 By similarity
Disulfide bond509 ↔ 553 By similarity
Disulfide bond512 ↔ 529 By similarity
Disulfide bond576 ↔ 624 By similarity

Experimental info

Sequence conflict4701S → F in AAC52964. Ref.1
Sequence conflict6611A → V in AAC52964. Ref.1
Sequence conflict6751A → G in AAC52964. Ref.1

Sequences

Sequence LengthMass (Da)Tools
O09126 [UniParc].

Last modified July 27, 2011. Version 2.
Checksum: B962D4E4CF37FFD9

FASTA86195,640
        10         20         30         40         50         60 
MRMCAPVRGL FLALVVVLRT AVAFAPVPRL TWEHGEVGLV QFHKPGIFNY SALLMSEDKD 

        70         80         90        100        110        120 
TLYVGAREAV FAVNALNISE KQHEVYWKVS EDKKSKCAEK GKSKQTECLN YIRVLQPLSS 

       130        140        150        160        170        180 
TSLYVCGTNA FQPTCDHLNL TSFKFLGKSE DGKGRCPFDP AHSYTSVMVG GELYSGTSYN 

       190        200        210        220        230        240 
FLGSEPIISR NSSHSPLRTE YAIPWLNEPS FVFADVIQKS PDGPEGEDDK VYFFFTEVSV 

       250        260        270        280        290        300 
EYEFVFKLMI PRVARVCKGD QGGLRTLQKK WTSFLKARLI CSKPDSGLVF NILQDVFVLR 

       310        320        330        340        350        360 
APGLKEPVFY AVFTPQLNNV GLSAVCAYTL ATVEAVFSRG KYMQSATVEQ SHTKWVRYNG 

       370        380        390        400        410        420 
PVPTPRPGAC IDSEARAANY TSSLNLPDKT LQFVKDHPLM DDSVTPIDNR PKLIKKDVNY 

       430        440        450        460        470        480 
TQIVVDRTQA LDGTFYDVMF ISTDRGALHK AVILTKEVHV IEETQLFRDS EPVLTLLLSS 

       490        500        510        520        530        540 
KKGRKFVYAG SNSGVVQAPL AFCEKHGSCE DCVLARDPYC AWSPAIKACV TLHQEEASSR 

       550        560        570        580        590        600 
GWIQDMSGDT SSCLDKSKES FNQHFFKHGG TAELKCFQKS NLARVVWKFQ NGELKAASPK 

       610        620        630        640        650        660 
YGFVGRKHLL IFNLSDGDSG VYQCLSEERV RNKTVSQLLA KHVLEVKMVP RTPPSPTSED 

       670        680        690        700        710        720 
AQTEGSKITS KMPVASTQGS SPPTPALWAT SPRAATLPPK SSSGTSCEPK MVINTVPQLH 

       730        740        750        760        770        780 
SEKTVYLKSS DNRLLMSLLL FIFVLFLCLF SYNCYKGYLP GQCLKFRSAL LLGKKTPKSD 

       790        800        810        820        830        840 
FSDLEQSVKE TLVEPGSFSQ QNGDHPKPAL DTGYETEQDT ITSKVPTDRE DSQRIDELSA 

       850        860 
RDKPFDVKCE LKFADSDADG D 

« Hide

References

« Hide 'large scale' references
[1]"Identification of a novel transmembrane semaphorin expressed on lymphocytes."
Furuyama T., Inagaki S., Kosugi A., Noda S., Saitoh S., Ogata M., Iwahashi Y., Miyazaki N., Hamaoka T., Tohyama M.
J. Biol. Chem. 271:33376-33381(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Strain: C57BL/6.
Tissue: Brain.
[2]Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Limb.
[4]"Plexin-B2, but not Plexin-B1, critically modulates neuronal migration and patterning of the developing nervous system in vivo."
Deng S., Hirschberg A., Worzfeld T., Penachioni J.Y., Korostylev A., Swiercz J.M., Vodrazka P., Mauti O., Stoeckli E.T., Tamagnone L., Offermanns S., Kuner R.
J. Neurosci. 27:6333-6347(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH PLXNB2.
[5]"Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins."
Wollscheid B., Bausch-Fluck D., Henderson C., O'Brien R., Bibel M., Schiess R., Aebersold R., Watts J.D.
Nat. Biotechnol. 27:378-386(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-77; ASN-379 AND ASN-419.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS26514.1.
RefSeqNP_001268809.1. NM_001281880.1.
NP_038688.2. NM_013660.4.
XP_006516945.1. XM_006516882.1.
XP_006516946.1. XM_006516883.1.
XP_006516947.1. XM_006516884.1.
XP_006516948.1. XM_006516885.1.
XP_006516949.1. XM_006516886.1.
XP_006516950.1. XM_006516887.1.
XP_006516951.1. XM_006516888.1.
XP_006516952.1. XM_006516889.1.
XP_006516953.1. XM_006516890.1.
UniGeneMm.33903.

3D structure databases

ProteinModelPortalO09126.
SMRO09126. Positions 24-648.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActO09126. 1 interaction.
MINTMINT-4996140.
STRING10090.ENSMUSP00000021900.

PTM databases

PhosphoSiteO09126.

Proteomic databases

PaxDbO09126.
PRIDEO09126.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000021900; ENSMUSP00000021900; ENSMUSG00000021451.
ENSMUST00000110039; ENSMUSP00000105666; ENSMUSG00000021451.
ENSMUST00000110040; ENSMUSP00000105667; ENSMUSG00000021451.
GeneID20354.
KEGGmmu:20354.
UCSCuc007qmn.1. mouse.

Organism-specific databases

CTD10507.
MGIMGI:109244. Sema4d.

Phylogenomic databases

eggNOGNOG326211.
GeneTreeENSGT00560000076864.
HOGENOMHOG000116087.
HOVERGENHBG061627.
InParanoidQ6GTM9.
KOK06521.
OMAIQDMSGD.
OrthoDBEOG71K62C.
TreeFamTF316102.

Gene expression databases

BgeeO09126.
GenevestigatorO09126.

Family and domain databases

Gene3D2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR016201. 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]
SMARTSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
PROSITEPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSEMA4D. mouse.
NextBio298221.
PROO09126.
SOURCESearch...

Entry information

Entry nameSEM4D_MOUSE
AccessionPrimary (citable) accession number: O09126
Secondary accession number(s): Q6GTM9
Entry history
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: July 27, 2011
Last modified: July 9, 2014
This is version 123 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