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O09126

- SEM4D_MOUSE

UniProt

O09126 - SEM4D_MOUSE

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Protein

Semaphorin-4D

Gene

Sema4d

Organism
Mus musculus (Mouse)
Status
Reviewed - 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 similarity

GO - Molecular functioni

  1. receptor binding Source: MGI
  2. semaphorin receptor binding Source: BHF-UCL
  3. transmembrane signaling receptor activity Source: UniProtKB

GO - Biological processi

  1. leukocyte aggregation Source: UniProtKB
  2. negative regulation of alkaline phosphatase activity Source: BHF-UCL
  3. negative regulation of cell adhesion Source: UniProtKB
  4. negative regulation of osteoblast differentiation Source: BHF-UCL
  5. negative regulation of peptidyl-tyrosine phosphorylation Source: BHF-UCL
  6. negative regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  7. ossification involved in bone maturation Source: BHF-UCL
  8. positive regulation of axonogenesis Source: MGI
  9. positive regulation of cell migration Source: BHF-UCL
  10. positive regulation of collateral sprouting Source: UniProtKB
  11. positive regulation of peptidyl-tyrosine phosphorylation Source: BHF-UCL
  12. positive regulation of phosphatidylinositol 3-kinase signaling Source: UniProtKB
  13. positive regulation of protein phosphorylation Source: UniProtKB
  14. positive regulation of Rho GTPase activity Source: BHF-UCL
  15. regulation of cell projection organization Source: UniProtKB
  16. regulation of cell shape Source: UniProtKB
  17. regulation of dendrite morphogenesis Source: UniProtKB
  18. semaphorin-plexin signaling pathway Source: UniProtKB
  19. semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis Source: BHF-UCL
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Neurogenesis

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 13

Organism-specific databases

MGIiMGI:109244. Sema4d.

Subcellular locationi

GO - Cellular componenti

  1. extracellular space Source: BHF-UCL
  2. integral component of plasma membrane Source: Ensembl
  3. membrane Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2323Sequence AnalysisAdd
BLAST
Chaini24 – 861838Semaphorin-4DPRO_0000032328Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi49 – 491N-linked (GlcNAc...)Sequence Analysis
Glycosylationi77 – 771N-linked (GlcNAc...)1 Publication
Disulfide bondi97 ↔ 108By similarity
Disulfide bondi126 ↔ 135By similarity
Glycosylationi139 – 1391N-linked (GlcNAc...)Sequence Analysis
Glycosylationi191 – 1911N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi257 ↔ 370By similarity
Disulfide bondi281 ↔ 326By similarity
Glycosylationi379 – 3791N-linked (GlcNAc...)1 Publication
Glycosylationi419 – 4191N-linked (GlcNAc...)1 Publication
Disulfide bondi503 ↔ 520By similarity
Disulfide bondi509 ↔ 553By similarity
Disulfide bondi512 ↔ 529By similarity
Disulfide bondi576 ↔ 624By similarity
Glycosylationi613 – 6131N-linked (GlcNAc...)Sequence Analysis
Glycosylationi632 – 6321N-linked (GlcNAc...)Sequence Analysis

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiO09126.
PaxDbiO09126.
PRIDEiO09126.

PTM databases

PhosphoSiteiO09126.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiO09126.
GenevestigatoriO09126.

Interactioni

Subunit structurei

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

Protein-protein interaction databases

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

Structurei

3D structure databases

ProteinModelPortaliO09126.
SMRiO09126. Positions 24-648.
ModBaseiSearch...
MobiDBiSearch...

Topological domain

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini24 – 733710ExtracellularSequence AnalysisAdd
BLAST
Topological domaini755 – 861107CytoplasmicSequence AnalysisAdd
BLAST

Transmembrane

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei734 – 75421HelicalSequence AnalysisAdd
BLAST

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini24 – 500477SemaPROSITE-ProRule annotationAdd
BLAST
Domaini502 – 55150PSIAdd
BLAST
Domaini555 – 63682Ig-like C2-typeAdd
BLAST

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

eggNOGiNOG326211.
GeneTreeiENSGT00760000118854.
HOGENOMiHOG000116087.
HOVERGENiHBG061627.
InParanoidiO09126.
KOiK06521.
OMAiIQDMSGD.
OrthoDBiEOG71K62C.
TreeFamiTF316102.

Family and domain databases

Gene3Di2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProiIPR007110. 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]
PANTHERiPTHR11036. PTHR11036. 1 hit.
PfamiPF01437. PSI. 1 hit.
PF01403. Sema. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view]
SUPFAMiSSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti470 – 4701S → F in AAC52964. (PubMed:8969198)Curated
Sequence conflicti661 – 6611A → V in AAC52964. (PubMed:8969198)Curated
Sequence conflicti675 – 6751A → G in AAC52964. (PubMed:8969198)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.
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.
UniGeneiMm.33903.

Genome annotation databases

EnsembliENSMUST00000021900; ENSMUSP00000021900; ENSMUSG00000021451.
ENSMUST00000110039; ENSMUSP00000105666; ENSMUSG00000021451.
ENSMUST00000110040; ENSMUSP00000105667; ENSMUSG00000021451.
GeneIDi20354.
KEGGimmu:20354.
UCSCiuc007qmn.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS26514.1.
RefSeqi NP_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.
UniGenei Mm.33903.

3D structure databases

ProteinModelPortali O09126.
SMRi O09126. Positions 24-648.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi O09126. 1 interaction.
MINTi MINT-4996140.
STRINGi 10090.ENSMUSP00000021900.

PTM databases

PhosphoSitei O09126.

Proteomic databases

MaxQBi O09126.
PaxDbi O09126.
PRIDEi O09126.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000021900 ; ENSMUSP00000021900 ; ENSMUSG00000021451 .
ENSMUST00000110039 ; ENSMUSP00000105666 ; ENSMUSG00000021451 .
ENSMUST00000110040 ; ENSMUSP00000105667 ; ENSMUSG00000021451 .
GeneIDi 20354.
KEGGi mmu:20354.
UCSCi uc007qmn.1. mouse.

Organism-specific databases

CTDi 10507.
MGIi MGI:109244. Sema4d.

Phylogenomic databases

eggNOGi NOG326211.
GeneTreei ENSGT00760000118854.
HOGENOMi HOG000116087.
HOVERGENi HBG061627.
InParanoidi O09126.
KOi K06521.
OMAi IQDMSGD.
OrthoDBi EOG71K62C.
TreeFami TF316102.

Miscellaneous databases

ChiTaRSi SEMA4D. mouse.
NextBioi 298221.
PROi O09126.
SOURCEi Search...

Gene expression databases

Bgeei O09126.
Genevestigatori O09126.

Family and domain databases

Gene3Di 2.130.10.10. 1 hit.
2.60.40.10. 1 hit.
InterProi IPR007110. 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 ]
PANTHERi PTHR11036. PTHR11036. 1 hit.
Pfami PF01437. PSI. 1 hit.
PF01403. Sema. 1 hit.
[Graphical view ]
SMARTi SM00409. IG. 1 hit.
SM00423. PSI. 1 hit.
SM00630. Sema. 1 hit.
[Graphical view ]
SUPFAMi SSF101912. SSF101912. 1 hit.
SSF103575. SSF103575. 1 hit.
PROSITEi PS50835. IG_LIKE. 1 hit.
PS51004. SEMA. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.

Entry informationi

Entry nameiSEM4D_MOUSE
AccessioniPrimary (citable) accession number: O09126
Secondary accession number(s): Q6GTM9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: July 27, 2011
Last modified: October 29, 2014
This is version 125 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