Sema5a sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sema5aprovided by MGI
Official Full Name: sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5Aprovided by MGI
Primary source: MGI:MGI:107556
See related: Ensembl:ENSMUSG00000022231 AllianceGenome:MGI:107556
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: semF; Semaf; 5930434A13; 9130201M22Rik
Summary: Enables axon guidance receptor activity and semaphorin receptor binding activity. Involved in several processes, including blood vessel endothelial cell proliferation involved in sprouting angiogenesis; negative regulation of endothelial cell apoptotic process; and regulation of signal transduction. Acts upstream of or within axonogenesis; branching involved in blood vessel morphogenesis; and detection of light stimulus involved in visual perception. Is integral component of membrane. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; hemolymphoid system; and sensory organ. Orthologous to human SEMA5A (semaphorin 5A). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in ovary adult (RPKM 13.8), limb E14.5 (RPKM 11.9) and 21 other tissues See more
Orthologs: human all
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Genomic context

Location:: 15 B3.1; 15 13.02 cM

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	15	NC_000081.7 (32244959..32696487)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	15	NC_000081.6 (32244813..32696341)

Chromosome 15 - NC_000081.7 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?

Mouse Sema5A negatively regulates synaptogenesis in early, developmentally born, hippocampal dentate granule cells.
Title: Semaphorin 5A inhibits synaptogenesis in early postnatal- and adult-born hippocampal dentate granule cells.
The results of this study concluded that the Sema5a mice do not meet the behavioral criteria for a mouse model of autism.
Title: Are Sema5a mutant mice a good model of autism? A behavioral analysis of sensory systems, emotionality and cognition.
Sema5A and Sema5B inhibit retinal neurite outgrowth through PlexinA1 and PlexinA3 receptors both in vitro and in vivo.
Title: Class 5 transmembrane semaphorins control selective Mammalian retinal lamination and function.
Data reveal that Sema5A is a novel proangiogenic molecule, inducing endothelial cell proliferation and migration and inhibiting apoptosis.
Title: Semaphorin 5A promotes angiogenesis by increasing endothelial cell proliferation, migration, and decreasing apoptosis.
A role of Sema5A in the remodeling of the cranial blood vessels was shown.
Title: Inactivation of the Sema5a gene results in embryonic lethality and defective remodeling of the cranial vascular system.
Semaphorin 5A (Sema5A) is a bifunctional guidance cue exerting both attractive and inhibitory effects on developing axons of the fasciculus retroflexus, a diencephalon fiber tract associated with limbic function.
Title: Semaphorin 5A is a bifunctional axon guidance cue regulated by heparan and chondroitin sulfate proteoglycans.
Plexin-B3 is a functional receptor for semaphorin 5A
Title: Plexin-B3 is a functional receptor for semaphorin 5A.
development of some CNS nerves requires inhibitory sheaths to maintain integrity, this is accomplished using molecules such as Sema5A that exhibit conserved inhibitory responses in the presence of impinging signals from multiple guidance molecules.
Title: Invariant Sema5A inhibition serves an ensheathing function during optic nerve development.

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Variation

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Alleles

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

Targeted (4) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D15Mit137 (e-PCR), detects polymorphism
- UniSTS:127498

fi29c12.x1 (e-PCR)
- UniSTS:197202

UniSTS:496014 (e-PCR)
- UniSTS:496014

Sema5a (e-PCR), detects polymorphism
- UniSTS:496014

D15Mit54 (e-PCR), detects polymorphism
- UniSTS:127673

AI464145 (e-PCR)
- UniSTS:160443

Sema5a (e-PCR), detects polymorphism
- UniSTS:545981

Sema5a (e-PCR), detects polymorphism
- UniSTS:532685

X97817 (e-PCR)
- UniSTS:125902

D15Mit126 (e-PCR), detects polymorphism
- UniSTS:127487

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables axon guidance receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables chemorepellent activity	IBA Inferred from Biological aspect of Ancestor more info
enables chondroitin sulfate proteoglycan binding	ISO Inferred from Sequence Orthology more info
enables heparan sulfate proteoglycan binding	ISO Inferred from Sequence Orthology more info
enables semaphorin receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables semaphorin receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables syndecan binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in axon extension	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axon extension	IGI Inferred from Genetic Interaction more info	PubMed
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axonal fasciculation	ISO Inferred from Sequence Orthology more info
involved_in blood vessel endothelial cell proliferation involved in sprouting angiogenesis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within branching involved in blood vessel morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within branching morphogenesis of an epithelial tube	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within detection of light stimulus involved in visual perception	IGI Inferred from Genetic Interaction more info	PubMed
involved_in diencephalon development	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 regulation of axon extension involved in axon guidance	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of endothelial cell apoptotic process	IDA Inferred from Direct Assay 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
acts_upstream_of_or_within neuron projection extension	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within neuron projection extension	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within neuron projection guidance	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of actin filament depolymerization	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of angiogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of axon extension involved in axon guidance	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of endothelial cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of endothelial cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of extracellular matrix disassembly	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IDA Inferred from Direct Assay 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 signal clustering	IDA Inferred from Direct Assay more info	PubMed
involved_in signal clustering	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	ISO Inferred from Sequence Orthology 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-5A

Names: M-Sema D; sema F; semaphorin F

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_009154.2 → NP_033180.2 semaphorin-5A precursor

See identical proteins and their annotated locations for NP_033180.2

Status: VALIDATED

Source sequence(s)

AC110236, AK141612, BB643469

Consensus CDS

CCDS37055.1

UniProtKB/Swiss-Prot

Q62217

UniProtKB/TrEMBL

Q3UPZ0

Related

ENSMUSP00000069024.7, ENSMUST00000067458.7

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:598 → 651

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat

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_000081.7 Reference GRCm39 C57BL/6J

Range

32244959..32696487

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036159282.1 → XP_036015175.1 semaphorin-5A isoform X1

UniProtKB/Swiss-Prot

Q62217

UniProtKB/TrEMBL

Q3UPZ0

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:598 → 651

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_030248431.2 → XP_030104291.1 semaphorin-5A isoform X1

UniProtKB/Swiss-Prot

Q62217

UniProtKB/TrEMBL

Q3UPZ0

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:598 → 651

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_030248430.2 → XP_030104290.1 semaphorin-5A isoform X1

UniProtKB/Swiss-Prot

Q62217

UniProtKB/TrEMBL

Q3UPZ0

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:598 → 651

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_036159281.1 → XP_036015174.1 semaphorin-5A isoform X1

UniProtKB/Swiss-Prot

Q62217

UniProtKB/TrEMBL

Q3UPZ0

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:598 → 651

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_036159283.1 → XP_036015176.1 semaphorin-5A isoform X2

UniProtKB/Swiss-Prot

Q62217

Conserved Domains (3) summary

smart00209
Location:441 → 494

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:329 → 376

PSI; Plexin repeat

cl15693
Location:1 → 328

Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
XM_011245340.2 → XP_011243642.1 semaphorin-5A isoform X1

See identical proteins and their annotated locations for XP_011243642.1

UniProtKB/Swiss-Prot

Q62217

UniProtKB/TrEMBL

Q3UPZ0

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:598 → 651

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_036159280.1 → XP_036015173.1 semaphorin-5A isoform X1

UniProtKB/Swiss-Prot

Q62217

UniProtKB/TrEMBL

Q3UPZ0

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:598 → 651

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat
XM_006520043.5 → XP_006520106.1 semaphorin-5A isoform X1

See identical proteins and their annotated locations for XP_006520106.1

UniProtKB/Swiss-Prot

Q62217

UniProtKB/TrEMBL

Q3UPZ0

Conserved Domains (3) summary

cd11263
Location:50 → 485

Sema_5A; The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A)

smart00209
Location:598 → 651

TSP1; Thrombospondin type 1 repeats

pfam01437
Location:486 → 533

PSI; Plexin repeat