O09126 (SEM4D_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	861 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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 process	Differentiation Neurogenesis
Cellular component	Cell membrane Membrane
Domain	Immunoglobulin domain Signal Transmembrane Transmembrane helix
Molecular function	Developmental protein
PTM	Disulfide bond Glycoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	leukocyte 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 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 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 cascade 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 involved in bone trabecula morphogenesis Inferred from mutant phenotype PubMed 22019888. Source: BHF-UCL
Cellular_component	extracellular space Inferred from direct assay PubMed 22019888. Source: BHF-UCL integral to plasma membrane Inferred from electronic annotation. Source: Compara membrane Traceable author statement PubMed 22019888. Source: BHF-UCL
Molecular_function	transmembrane signaling receptor activity Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Signal peptide	1 – 23	23	Potential
	Chain	24 – 861	838	Semaphorin-4D		PRO_0000032328
Regions
	Topological domain	24 – 733	710	Extracellular Potential
	Transmembrane	734 – 754	21	Helical; Potential
	Topological domain	755 – 861	107	Cytoplasmic Potential
	Domain	24 – 500	477	Sema
	Domain	502 – 551	50	PSI
	Domain	555 – 636	82	Ig-like C2-type
Amino acid modifications
	Glycosylation	49	1	N-linked (GlcNAc...) Potential
	Glycosylation	77	1	N-linked (GlcNAc...) Ref.5
	Glycosylation	139	1	N-linked (GlcNAc...) Potential
	Glycosylation	191	1	N-linked (GlcNAc...) Potential
	Glycosylation	379	1	N-linked (GlcNAc...) Ref.5
	Glycosylation	419	1	N-linked (GlcNAc...) Ref.5
	Glycosylation	613	1	N-linked (GlcNAc...) Potential
	Glycosylation	632	1	N-linked (GlcNAc...) Potential
	Disulfide bond	97 ↔ 108		By similarity
	Disulfide bond	126 ↔ 135		By similarity
	Disulfide bond	257 ↔ 370		By similarity
	Disulfide bond	281 ↔ 326		By similarity
	Disulfide bond	503 ↔ 520		By similarity
	Disulfide bond	509 ↔ 553		By similarity
	Disulfide bond	512 ↔ 529		By similarity
	Disulfide bond	576 ↔ 624		By similarity
Experimental info
	Sequence conflict	470	1	S → F in AAC52964. Ref.1
	Sequence conflict	661	1	A → V in AAC52964. Ref.1
	Sequence conflict	675	1	A → G in AAC52964. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	O09126 [UniParc]. Last modified July 27, 2011. Version 2. Checksum: B962D4E4CF37FFD9	FASTA	861	95,640
	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

References

	« Hide 'large scale' referencesShow '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, MASS SPECTROMETRY.
+	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.
IPI	IPI00114274.
RefSeq	NP_038688.2. NM_013660.3.
UniGene	Mm.33903.
3D structure databases
ProteinModelPortal	O09126.
SMR	O09126. Positions 24-648.
ModBase	Search...
Protein-protein interaction databases
IntAct	O09126. 1 interaction.
STRING	10090.ENSMUSP00000021900.
PTM databases
PhosphoSite	O09126.
Proteomic databases
PaxDb	O09126.
PRIDE	O09126.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000021900; ENSMUSP00000021900; ENSMUSG00000021451. ENSMUST00000110039; ENSMUSP00000105666; ENSMUSG00000021451. ENSMUST00000110040; ENSMUSP00000105667; ENSMUSG00000021451.
GeneID	20354.
KEGG	mmu:20354.
Organism-specific databases
CTD	10507.
MGI	MGI:109244. Sema4d.
Phylogenomic databases
eggNOG	NOG326211.
GeneTree	ENSGT00560000076864.
HOGENOM	HOG000116087.
HOVERGEN	HBG061627.
InParanoid	Q6GTM9.
KO	K06521.
OMA	IQDMSGD.
OrthoDB	EOG43N7C4.
Gene expression databases
ArrayExpress	O09126.
Bgee	O09126.
Genevestigator	O09126.
GermOnline	ENSMUSG00000021451. Mus musculus.
Family and domain databases
Gene3D	2.130.10.10. 1 hit. 2.60.40.10. 1 hit.
InterPro	IPR007110. Ig-like_dom. IPR013783. Ig-like_fold. IPR003599. Ig_sub. IPR003659. Plexin-like. IPR016201. Plexin-like_fold. IPR002165. Plexin_repeat. IPR027231. Semaphorin. IPR001627. Semaphorin/CD100_Ag. IPR015943. WD40/YVTN_repeat-like_dom. [Graphical view]
PANTHER	PTHR11036. PTHR11036. 1 hit.
Pfam	PF01437. PSI. 1 hit. PF01403. Sema. 1 hit. [Graphical view]
SMART	SM00409. IG. 1 hit. SM00423. PSI. 1 hit. SM00630. Sema. 1 hit. [Graphical view]
SUPFAM	SSF103575. Plexin-like_fold. 1 hit. SSF101912. Sema. 1 hit.
PROSITE	PS50835. IG_LIKE. 1 hit. PS51004. SEMA. 1 hit. [Graphical view]
ProtoNet	Search...
Other
ChiTaRS	SEMA4D. mouse.
NextBio	298221.
SOURCE	Search...

Entry information

Entry name

SEM4D_MOUSE

Accession

Primary (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:	May 1, 2013
This is version 112 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program