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Sema3a sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A [ Mus musculus (house mouse) ]

Gene ID: 20346, updated on 22-Jan-2023

Summary

Official Symbol
Sema3aprovided by MGI
Official Full Name
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Aprovided by MGI
Primary source
MGI:MGI:107558
See related
Ensembl:ENSMUSG00000028883 AllianceGenome:MGI:107558
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
SemD; SEMA1; Semad; coll-1; Hsema-I
Summary
Enables chemorepellent activity; neuropilin binding activity; and semaphorin receptor binding activity. Involved in several processes, including nervous system development; positive regulation of male gonad development; and ventral trunk neural crest cell migration. Acts upstream of or within several processes, including dichotomous subdivision of terminal units involved in salivary gland branching; generation of neurons; and negative regulation of epithelial cell migration. Located in extracellular space. Is expressed in several structures, including alimentary system; central nervous system; embryo mesenchyme; metanephros; and sensory organ. Human ortholog(s) of this gene implicated in hypogonadotropic hypogonadism 16 with or without anosmia. Orthologous to human SEMA3A (semaphorin 3A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in limb E14.5 (RPKM 3.0), bladder adult (RPKM 3.0) and 16 other tissues See more
Orthologs
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Genomic context

See Sema3a in Genome Data Viewer
Location:
5; 5 A1
Exon count:
25
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (13174789..13653453)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (13124822..13603485)

Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene predicted gene 6641 Neighboring gene cytochrome c, somatic pseudogene Neighboring gene predicted gene, 52804 Neighboring gene anaphase-promoting complex subunit 5 pseudogene Neighboring gene predicted gene 6647

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables chemorepellent activity IDA
Inferred from Direct Assay
more info
PubMed 
enables neuropilin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables neuropilin binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 
Process Evidence Code Pubs
involved_in apoptotic process ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of axon extension IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of axon extension IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of axon extension involved in axon guidance IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of axon extension involved in axon guidance IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in axon extension involved in axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within axon guidance IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within axon guidance ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within axonal fasciculation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in axonogenesis involved in innervation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in basal dendrite arborization IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in branchiomotor neuron axon guidance 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 dendrite morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within dichotomous subdivision of terminal units involved in salivary gland branching IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of epithelial cell migration IDA
Inferred from Direct Assay
more info
PubMed 
involved_in facial nerve structural organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in facioacoustic ganglion development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in gonadotrophin-releasing hormone neuronal migration to the hypothalamus IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in maintenance of synapse structure IDA
Inferred from Direct Assay
more info
PubMed 
involved_in maintenance of synapse structure IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in motor neuron axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in motor neuron axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 
acts_upstream_of_or_within negative chemotaxis IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within negative regulation of axon extension IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within negative regulation of axon extension IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in negative regulation of axon extension 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 
acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within negative regulation of axon extension involved in axon guidance IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within negative regulation of epithelial cell migration IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of neuron projection development ISO
Inferred from Sequence Orthology
more info
 
involved_in nerve development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within nervous system development IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in neural crest cell migration involved in autonomic nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in neural crest cell migration involved in sympathetic nervous system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in neuron migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in olfactory bulb development ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of male gonad development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of neuron migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of neuron migration IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in regulation of axon extension involved in axon guidance IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of axon extension involved in axon guidance ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of heart rate IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within semaphorin-plexin signaling pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in semaphorin-plexin signaling pathway involved in axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in semaphorin-plexin signaling pathway involved in neuron projection guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in sympathetic ganglion development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in sympathetic neuron projection extension IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in sympathetic neuron projection guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in synaptic target recognition IDA
Inferred from Direct Assay
more info
PubMed 
involved_in synaptic target recognition IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in trigeminal ganglion development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in trigeminal nerve structural organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in ventral trunk neural crest cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
is_active_in axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in axon ISO
Inferred from Sequence Orthology
more info
 
is_active_in cerebellar climbing fiber to Purkinje cell synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cerebellar climbing fiber to Purkinje cell synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in dendrite ISO
Inferred from Sequence Orthology
more info
 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular region TAS
Traceable Author Statement
more info
 
located_in extracellular space HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
semaphorin-3A
Names
collapsin-1
sema D
sema III
semaphorin III
semaphorin-D

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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)

  1. NM_001243072.1NP_001230001.1  semaphorin-3A precursor

    See identical proteins and their annotated locations for NP_001230001.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC022368, BC090844
    Consensus CDS
    CCDS19092.1
    UniProtKB/Swiss-Prot
    O08665
    UniProtKB/TrEMBL
    A0A803Z7F8, A0A8C6HA71
    Related
    ENSMUSP00000092621.5, ENSMUST00000095012.11
    Conserved Domains (3) summary
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:580671
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  2. NM_001243073.1NP_001230002.1  semaphorin-3A precursor

    See identical proteins and their annotated locations for NP_001230002.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC022368, AK140817
    Consensus CDS
    CCDS19092.1
    UniProtKB/Swiss-Prot
    O08665
    UniProtKB/TrEMBL
    A0A803Z7F8, A0A8C6HA71
    Related
    ENSMUSP00000128153.3, ENSMUST00000137798.10
    Conserved Domains (3) summary
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:580671
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  3. NM_009152.4NP_033178.2  semaphorin-3A precursor

    See identical proteins and their annotated locations for NP_033178.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC022368, AC121125, BC057588
    Consensus CDS
    CCDS19092.1
    UniProtKB/Swiss-Prot
    O08665
    UniProtKB/TrEMBL
    A0A803Z7F8, A0A8C6HA71
    Related
    ENSMUSP00000030714.9, ENSMUST00000030714.9
    Conserved Domains (3) summary
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:580671
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000071.7 Reference GRCm39 C57BL/6J

    Range
    13174789..13653453
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006503557.5XP_006503620.2  semaphorin-3A isoform X1

    UniProtKB/TrEMBL
    A0A803Z7F8, A0A8C6HA71
    Conserved Domains (3) summary
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:580671
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  2. XM_011240665.4XP_011238967.2  semaphorin-3A isoform X1

    UniProtKB/TrEMBL
    A0A803Z7F8, A0A8C6HA71
    Conserved Domains (3) summary
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:580671
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  3. XM_036164936.1XP_036020829.1  semaphorin-3A isoform X1

    UniProtKB/TrEMBL
    A0A803Z7F8, A0A8C6HA71
    Conserved Domains (3) summary
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:580671
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  4. XM_036164937.1XP_036020830.1  semaphorin-3A isoform X1

    UniProtKB/TrEMBL
    A0A803Z7F8, A0A8C6HA71
    Conserved Domains (3) summary
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:580671
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  5. XM_006503559.3XP_006503622.2  semaphorin-3A isoform X1

    UniProtKB/TrEMBL
    A0A803Z7F8, A0A8C6HA71
    Conserved Domains (3) summary
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:580671
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  6. XM_036164935.1XP_036020828.1  semaphorin-3A isoform X1

    UniProtKB/TrEMBL
    A0A803Z7F8, A0A8C6HA71
    Conserved Domains (3) summary
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:580671
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  7. XM_006503558.5XP_006503621.2  semaphorin-3A isoform X1

    UniProtKB/TrEMBL
    A0A803Z7F8, A0A8C6HA71
    Conserved Domains (3) summary
    cd11249
    Location:26518
    Sema_3A; The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A)
    smart00423
    Location:516552
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:580671
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3