Sema4a sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sema4aprovided by MGI
Official Full Name: sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Aprovided by MGI
Primary source: MGI:MGI:107560
See related: Ensembl:ENSMUSG00000028064 AllianceGenome:MGI:107560
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: SemB; Semab
Summary: Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Involved in several processes, including T-helper 1 cell differentiation; negative regulation of angiogenesis; and positive regulation of synapse assembly. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Is expressed in several structures, including blood vessel; central nervous system; primitive ventricle; retina; and ureteric trunk. Human ortholog(s) of this gene implicated in cone-rod dystrophy 10 and retinitis pigmentosa 35. Orthologous to human SEMA4A (semaphorin 4A). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in colon adult (RPKM 43.5), duodenum adult (RPKM 41.8) and 25 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 F1; 3 38.83 cM

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (88343266..88368500, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (88435959..88461182, complement)

Chromosome 3 - NC_000069.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

Sema4A is implicated in the acceleration of Th17 cell-mediated neuroinflammation in the effector phase.
Title: Sema4A is implicated in the acceleration of Th17 cell-mediated neuroinflammation in the effector phase.
We highlight a common but age-related Sema4a-mediated pathway by which plasmacytoid dendritic cells and microbial colonization induce T reg cell expansion to protect against severe bronchiolitis and subsequent asthma.
Title: Plasmacytoid dendritic cells protect from viral bronchiolitis and asthma through semaphorin 4a-mediated T reg expansion.
Sema4A functions through postsynaptic Plexin-B2 for excitatory synapse development.
Title: Class 4 Semaphorins and Plexin-B receptors regulate GABAergic and glutamatergic synapse development in the mammalian hippocampus.
Suggest a role for Plexin-B1 as a ligand and Sema4A as a receptor and characterize a reverse signaling pathway downstream of Sema4A regulating cell migration via Scrib.
Title: A reverse signaling pathway downstream of Sema4A controls cell migration via Scrib.
SEMA4A is required for optimal activation of mTORC1 in CD8+ T cells.
Title: mTOR Complex Signaling through the SEMA4A-Plexin B2 Axis Is Required for Optimal Activation and Differentiation of CD8+ T Cells.
Treg-cell stability can be subverted in certain inflammatory sites, but is maintained by a Sema4a-Nrp1 axis-- this pathway is a potential therapeutic target that could limit Treg-cell-mediated tumour-induced tolerance without inducing autoimmunity
Title: Stability and function of regulatory T cells is maintained by a neuropilin-1-semaphorin-4a axis.
Data indicate that both semaphorin 4A mRNA and protein were clearly detected on the earliest progenitors and were downregulated through thymic development.
Title: Semaphorin 4A is dynamically regulated during thymocyte development in mice.
These results indicate the importance of the Sema4A protein conformation in human and mouse retina homeostasis.
Title: A point mutation in Semaphorin 4A associates with defective endosomal sorting and causes retinal degeneration.
A fraction of Sema4a-deficient transgenic BALB/c mice spontaneously develop skin lesions resembling atopic dermatitis (AD) in humans.
Title: An inhibitory role for Sema4A in antigen-specific allergic asthma.
These data provide a new insight into Sema4A biology and define Sema4A as an important regulator of Th2-driven lung pathophysiology.
Title: Neuroimmune semaphorin 4A downregulates the severity of allergic response.

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Variation

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Alleles

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

Gene trapped (1) 1 citation
Targeted (7) 1 citation
Endonuclease-mediated (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI132332 (e-PCR)
- UniSTS:185541

X85991 (e-PCR)
- UniSTS:185542

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in T cell differentiation involved in immune response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in T-helper 1 cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within adaptive immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within angiogenesis	IEA Inferred from Electronic Annotation more info
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in axonogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within immune system process	IEA Inferred from Electronic Annotation 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
involved_in negative regulation of angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
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
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of excitatory synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of inhibitory synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell shape	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of endothelial cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in semaphorin-plexin signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in semaphorin-plexin signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in semaphorin-plexin signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in membrane	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: semaphorin-4A

Names: sema B; semaphorin-B

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_001163489.2 → NP_001156961.1 semaphorin-4A precursor

See identical proteins and their annotated locations for NP_001156961.1

Status: VALIDATED

Source sequence(s)

AC102388

Consensus CDS

CCDS17475.1

UniProtKB/Swiss-Prot

D3Z5L2, Q62178

UniProtKB/TrEMBL

D3YWV5

Related

ENSMUSP00000125909.2, ENSMUST00000166237.8

Conserved Domains (4) summary

smart00423
Location:496 → 540

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:572 → 580

Ig; Ig strand B [structural motif]

cl11960
Location:570 → 637

Ig; Immunoglobulin domain

cl15693
Location:55 → 495

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
NM_001163490.2 → NP_001156962.1 semaphorin-4A precursor

See identical proteins and their annotated locations for NP_001156962.1

Status: VALIDATED

Source sequence(s)

AC102388

Consensus CDS

CCDS17475.1

UniProtKB/Swiss-Prot

D3Z5L2, Q62178

UniProtKB/TrEMBL

D3YWV5

Related

ENSMUSP00000128510.2, ENSMUST00000165898.8

Conserved Domains (4) summary

smart00423
Location:496 → 540

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:572 → 580

Ig; Ig strand B [structural motif]

cl11960
Location:570 → 637

Ig; Immunoglobulin domain

cl15693
Location:55 → 495

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
NM_001163491.2 → NP_001156963.1 semaphorin-4A precursor

See identical proteins and their annotated locations for NP_001156963.1

Status: VALIDATED

Source sequence(s)

AC102388

Consensus CDS

CCDS17475.1

UniProtKB/Swiss-Prot

D3Z5L2, Q62178

UniProtKB/TrEMBL

D3YWV5

Related

ENSMUSP00000128887.2, ENSMUST00000169222.8

Conserved Domains (4) summary

smart00423
Location:496 → 540

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:572 → 580

Ig; Ig strand B [structural motif]

cl11960
Location:570 → 637

Ig; Immunoglobulin domain

cl15693
Location:55 → 495

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
NM_001428657.1 → NP_001415586.1 semaphorin-4A precursor

Status: VALIDATED

Source sequence(s)

AC102388

UniProtKB/Swiss-Prot

D3Z5L2, Q62178
NM_001428658.1 → NP_001415587.1 semaphorin-4A precursor

Status: VALIDATED

Source sequence(s)

AC102388

UniProtKB/Swiss-Prot

D3Z5L2, Q62178
NM_013658.3 → NP_038686.3 semaphorin-4A precursor

See identical proteins and their annotated locations for NP_038686.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript. All four variants encode the same protein.

Source sequence(s)

AK077976, AK153164, BY201883

Consensus CDS

CCDS17475.1

UniProtKB/Swiss-Prot

D3Z5L2, Q62178

UniProtKB/TrEMBL

D3YWV5

Related

ENSMUSP00000029700.6, ENSMUST00000029700.12

Conserved Domains (4) summary

smart00423
Location:496 → 540

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:572 → 580

Ig; Ig strand B [structural motif]

cl11960
Location:570 → 637

Ig; Immunoglobulin domain

cl15693
Location:55 → 495

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

88343266..88368500 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036162974.1 → XP_036018867.1 semaphorin-4A isoform X3

Conserved Domains (4) summary

smart00423
Location:496 → 540

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:572 → 580

Ig; Ig strand B [structural motif]

cl11960
Location:570 → 637

Ig; Immunoglobulin domain

cl15693
Location:55 → 495

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_006501190.4 → XP_006501253.1 semaphorin-4A isoform X4

See identical proteins and their annotated locations for XP_006501253.1

UniProtKB/TrEMBL

D3YWV5

Conserved Domains (3) summary

smart00423
Location:327 → 371

PSI; domain found in Plexins, Semaphorins and Integrins

cl11960
Location:396 → 468

Ig; Immunoglobulin domain

cl15693
Location:1 → 326

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_036162971.1 → XP_036018864.1 semaphorin-4A isoform X2

UniProtKB/TrEMBL

D3YWV5

Conserved Domains (4) summary

smart00423
Location:520 → 564

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:596 → 604

Ig; Ig strand B [structural motif]

cl11960
Location:594 → 661

Ig; Immunoglobulin domain

cl15693
Location:79 → 519

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_036162972.1 → XP_036018865.1 semaphorin-4A isoform X3

UniProtKB/Swiss-Prot

D3Z5L2, Q62178

UniProtKB/TrEMBL

D3YWV5

Conserved Domains (4) summary

smart00423
Location:496 → 540

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:572 → 580

Ig; Ig strand B [structural motif]

cl11960
Location:570 → 637

Ig; Immunoglobulin domain

cl15693
Location:55 → 495

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_006501187.4 → XP_006501250.1 semaphorin-4A isoform X1

Conserved Domains (3) summary

smart00423
Location:534 → 578

PSI; domain found in Plexins, Semaphorins and Integrins

cl11960
Location:603 → 675

Ig; Immunoglobulin domain

cl15693
Location:93 → 533

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_006501189.3 → XP_006501252.1 semaphorin-4A isoform X3

See identical proteins and their annotated locations for XP_006501252.1

UniProtKB/Swiss-Prot

D3Z5L2, Q62178

UniProtKB/TrEMBL

D3YWV5

Conserved Domains (4) summary

smart00423
Location:496 → 540

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:572 → 580

Ig; Ig strand B [structural motif]

cl11960
Location:570 → 637

Ig; Immunoglobulin domain

cl15693
Location:55 → 495

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_011240051.3 → XP_011238353.1 semaphorin-4A isoform X3

Conserved Domains (4) summary

smart00423
Location:496 → 540

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:572 → 580

Ig; Ig strand B [structural motif]

cl11960
Location:570 → 637

Ig; Immunoglobulin domain

cl15693
Location:55 → 495

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_006501191.4 → XP_006501254.1 semaphorin-4A isoform X4

See identical proteins and their annotated locations for XP_006501254.1

UniProtKB/TrEMBL

D3YWV5

Conserved Domains (3) summary

smart00423
Location:327 → 371

PSI; domain found in Plexins, Semaphorins and Integrins

cl11960
Location:396 → 468

Ig; Immunoglobulin domain

cl15693
Location:1 → 326

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_006501188.5 → XP_006501251.1 semaphorin-4A isoform X2

UniProtKB/TrEMBL

D3YWV5

Conserved Domains (4) summary

smart00423
Location:520 → 564

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:596 → 604

Ig; Ig strand B [structural motif]

cl11960
Location:594 → 661

Ig; Immunoglobulin domain

cl15693
Location:79 → 519

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_036162975.1 → XP_036018868.1 semaphorin-4A isoform X5

UniProtKB/TrEMBL

D3YWV5

Conserved Domains (4) summary

smart00423
Location:305 → 349

PSI; domain found in Plexins, Semaphorins and Integrins

cd00096
Location:381 → 389

Ig; Ig strand B [structural motif]

cl11960
Location:379 → 446

Ig; Immunoglobulin domain

cl15693
Location:1 → 304

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins