Sema4d sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sema4dprovided by MGI
Official Full Name: sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Dprovided by MGI
Primary source: MGI:MGI:109244
See related: Ensembl:ENSMUSG00000021451 AllianceGenome:MGI:109244
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: CD100; Semaj; Semcl2; coll-4; Semacl2
Summary: Enables semaphorin receptor binding activity. Involved in several processes, including negative regulation of osteoblast differentiation; positive regulation of inhibitory synapse assembly; and regulation of phosphate metabolic process. Acts upstream of or within positive regulation of axonogenesis. Located in extracellular space. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; hemolymphoid system; and respiratory system. Orthologous to human SEMA4D (semaphorin 4D). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in thymus adult (RPKM 32.3), spleen adult (RPKM 22.4) and 23 other tissues See more
Orthologs: human all
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Genomic context

Location:: 13; 13 A5

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	13	NC_000079.7 (51839565..51947823, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	13	NC_000079.6 (51685529..51793678, complement)

Chromosome 13 - NC_000079.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Semaphorin 4D is upregulated in neurons of diseased brains and triggers astrocyte reactivity.
Title: Semaphorin 4D is upregulated in neurons of diseased brains and triggers astrocyte reactivity.
Inhibition of Semaphorin 4D/Plexin-B1 signaling inhibits the subchondral bone loss in early-stage osteoarthritis of the temporomandibular joint.
Title: Inhibition of Semaphorin 4D/Plexin-B1 signaling inhibits the subchondral bone loss in early-stage osteoarthritis of the temporomandibular joint.
Anti-Semaphorin 4D Rescues Motor, Cognitive, and Respiratory Phenotypes in a Rett Syndrome Mouse Model.
Title: Anti-Semaphorin 4D Rescues Motor, Cognitive, and Respiratory Phenotypes in a Rett Syndrome Mouse Model.
Inhibition of Sema4D/PlexinB1 signaling alleviates vascular dysfunction in diabetic retinopathy.
Title: Inhibition of Sema4D/PlexinB1 signaling alleviates vascular dysfunction in diabetic retinopathy.
Sema4d role in the regulation of nitric oxide production in the microglia.The enhancement of nitric oxide production by Sema4D is involved in partial Erk1 and Erk2 inhibition and up-regulation of Iinterferon-beta.
Title: Upregulation of IFN-β induced by Sema4D-dependent partial Erk1/2 inhibition promotes NO production in microglia.
Sema4D regulates microglial proliferation in part by regulating the competitive balance of l-arginine metabolism.
Title: Changes in L-arginine metabolism by Sema4D deficiency induce promotion of microglial proliferation in ischemic cortex.
Sema4D induces the clustering of inhibitory presynaptic components via Plexin-B1.
Title: Class 4 Semaphorins and Plexin-B receptors regulate GABAergic and glutamatergic synapse development in the mammalian hippocampus.
These results demonstrate a novel physiological function for sema4D/plxnB1 signaling in retinal pigment epithelium phagocytosis.
Title: Semaphorin4D-PlexinB1 Signaling Attenuates Photoreceptor Outer Segment Phagocytosis by Reducing Rac1 Activity of RPE Cells.
suggest that STING activates ADAM17 and that this activation produces soluble proinflammatory SEMA4D independently of the TBK1/IRF3-mediated transcriptional pathway
Title: Activation of stimulator of interferon genes (STING) induces ADAM17-mediated shedding of the immune semaphorin SEMA4D.
These results reveal a novel signaling network, the Sema4D-RhoA-Akt signal cascade, that coordinates cellular function and morphology and highlights the importance of specific spatiotemporally restricted components of a signaling pathway in the regulation of ameloblast differentiation.
Title: The Semaphorin 4D-RhoA-Akt Signal Cascade Regulates Enamel Matrix Secretion in Coordination With Cell Polarization During Ameloblast Differentiation.

Submit: New GeneRIF Correction See all GeneRIFs (48)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (4) 1 citation
Endonuclease-mediated (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:224412

D13Mit139 (e-PCR), detects polymorphism
- UniSTS:116408

Homology

Homologs of the Sema4d gene: The Sema4d gene is conserved in human, chimpanzee, Rhesus monkey, dog, rat, chicken, and zebrafish.
Orthologs from Annotation Pipeline: 469 organisms have orthologs with human gene Sema4d
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables semaphorin receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables semaphorin receptor binding	ISO Inferred from Sequence Orthology more info
enables signaling receptor activity	ISO Inferred from Sequence Orthology more info
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor binding	ISO Inferred from Sequence Orthology more info
enables transmembrane signaling receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of axonogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of axonogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in leukocyte aggregation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
involved_in negative chemotaxis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of alkaline phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of alkaline phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of alkaline phosphatase activity	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of axon extension involved in axon guidance	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of osteoblast differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
involved_in neural crest cell migration	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in ossification involved in bone maturation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in ossification involved in bone maturation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ossification involved in bone maturation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of GTPase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of GTPase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of GTPase activity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of axonogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of axonogenesis	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of collateral sprouting	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of inhibitory synapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of inhibitory synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of phosphatidylinositol 3-kinase signaling	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell projection organization	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell shape	ISO Inferred from Sequence Orthology more info
involved_in regulation of dendrite morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in semaphorin-plexin signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: semaphorin-4D

Names: M-sema G; sema J; semaphorin H; semaphorin-C-like 2; semaphorin-J

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001281880.2 → NP_001268809.1 semaphorin-4D isoform 1 precursor

See identical proteins and their annotated locations for NP_001268809.1

Status: VALIDATED

Source sequence(s)

AC126247, AC126547

Consensus CDS

CCDS26514.1

UniProtKB/Swiss-Prot

O09126, Q6GTM9

Related

ENSMUSP00000105667.3, ENSMUST00000110040.9

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
NM_001378313.1 → NP_001365242.1 semaphorin-4D isoform 1 precursor

Status: VALIDATED

Source sequence(s)

AC126547

UniProtKB/Swiss-Prot

Q6GTM9

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
NM_001378314.1 → NP_001365243.1 semaphorin-4D isoform 1 precursor

Status: VALIDATED

Source sequence(s)

AC126547

UniProtKB/Swiss-Prot

Q6GTM9

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
NM_001378315.1 → NP_001365244.1 semaphorin-4D isoform 1 precursor

Status: VALIDATED

Source sequence(s)

AC126547

UniProtKB/Swiss-Prot

Q6GTM9

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
NM_001378316.1 → NP_001365245.1 semaphorin-4D isoform 1 precursor

Status: VALIDATED

Source sequence(s)

AC126547

UniProtKB/Swiss-Prot

Q6GTM9

Related

ENSMUSP00000105666.2, ENSMUST00000110039.2

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
NM_001378317.1 → NP_001365246.1 semaphorin-4D isoform 2 precursor

Status: VALIDATED

Source sequence(s)

AC126247, AC126547

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
NM_001378318.1 → NP_001365247.1 semaphorin-4D isoform 2 precursor

Status: VALIDATED

Source sequence(s)

AC126547

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
NM_001378319.1 → NP_001365248.1 semaphorin-4D isoform 2 precursor

Status: VALIDATED

Source sequence(s)

AC126547

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
NM_001378320.1 → NP_001365249.1 semaphorin-4D isoform 3 precursor

Status: VALIDATED

Source sequence(s)

AC126247, AC126547

Conserved Domains (2) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat
NM_001378321.1 → NP_001365250.1 semaphorin-4D isoform 3 precursor

Status: VALIDATED

Source sequence(s)

AC126247, AC126547

Conserved Domains (2) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat
NM_001378322.1 → NP_001365251.1 semaphorin-4D isoform 3 precursor

Status: VALIDATED

Source sequence(s)

AC126547

Conserved Domains (2) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat
NM_001378323.1 → NP_001365252.1 semaphorin-4D isoform 3 precursor

Status: VALIDATED

Source sequence(s)

AC126547

Conserved Domains (2) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat
NM_001378324.1 → NP_001365253.1 semaphorin-4D isoform 4 precursor

Status: VALIDATED

Source sequence(s)

AC126247, AC126547

Conserved Domains (2) summary

cd11259
Location:31 → 499

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:501 → 546

PSI; Plexin repeat
NM_001378325.1 → NP_001365254.1 semaphorin-4D isoform 5

Status: VALIDATED

Source sequence(s)

AC126547

Related

ENSMUSP00000105669.3, ENSMUST00000110042.3

Conserved Domains (2) summary

cd00096
Location:63 → 71

Ig; Ig strand B [structural motif]

cl11960
Location:55 → 139

Ig; Immunoglobulin domain
NM_013660.5 → NP_038688.2 semaphorin-4D isoform 1 precursor

See identical proteins and their annotated locations for NP_038688.2

Status: VALIDATED

Source sequence(s)

AC126247, AC126547

Consensus CDS

CCDS26514.1

UniProtKB/Swiss-Prot

O09126, Q6GTM9

Related

ENSMUSP00000021900.8, ENSMUST00000021900.14

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000079.7 Reference GRCm39 C57BL/6J

Range

51839565..51947823 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036157947.1 → XP_036013840.1 semaphorin-4D isoform X3

Conserved Domains (2) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat
XM_036157945.1 → XP_036013838.1 semaphorin-4D isoform X1

Conserved Domains (4) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat

cd00096
Location:569 → 577

Ig; Ig strand B [structural motif]

cl11960
Location:563 → 646

Ig; Immunoglobulin domain
XM_036157946.1 → XP_036013839.1 semaphorin-4D isoform X2

Conserved Domains (2) summary

cd11259
Location:31 → 501

Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

pfam01437
Location:503 → 548

PSI; Plexin repeat
XM_036157948.1 → XP_036013841.1 semaphorin-4D isoform X4

Conserved Domains (2) summary

cd00096
Location:63 → 71

Ig; Ig strand B [structural motif]

cl11960
Location:55 → 139

Ig; Immunoglobulin domain