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Sema3f sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [ Mus musculus (house mouse) ]

Gene ID: 20350, updated on 28-Dec-2022

Summary

Official Symbol
Sema3fprovided by MGI
Official Full Name
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Fprovided by MGI
Primary source
MGI:MGI:1096347
See related
Ensembl:ENSMUSG00000034684 AllianceGenome:MGI:1096347
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
Sema4; Semak
Summary
Enables chemorepellent activity. Involved in nervous system development; regulation of postsynapse organization; and ventral trunk neural crest cell migration. Acts upstream of or within generation of neurons; negative chemotaxis; and neural crest cell migration. Located in extracellular space. Is active in glutamatergic synapse. Is expressed in several structures, including alimentary system; brain; genitourinary system; respiratory system; and sensory organ. Orthologous to human SEMA3F (semaphorin 3F). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in lung adult (RPKM 77.6), limb E14.5 (RPKM 39.8) and 19 other tissues See more
Orthologs
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Genomic context

See Sema3f in Genome Data Viewer
Location:
9; 9 F1
Exon count:
21
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (107558698..107587674, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (107681499..107710475, complement)

Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene solute carrier family 38, member 3 Neighboring gene G protein subunit alpha transducin 1 Neighboring gene predicted gene, 51690 Neighboring gene predicted gene, 34605 Neighboring gene RNA binding motif protein 5

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)
  • Gene trapped (1) 
  • Targeted (9)  1 citation
  • Endonuclease-mediated (1) 

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 chemorepellent activity ISO
Inferred from Sequence Orthology
more info
PubMed 
enables semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
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 
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
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 ISO
Inferred from Sequence Orthology
more info
PubMed 
involved_in branchiomotor neuron axon guidance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in facial nerve structural organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in locomotion IC
Inferred by Curator
more info
PubMed 
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within negative chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within negative chemotaxis IGI
Inferred from Genetic Interaction
more info
PubMed 
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 
involved_in nerve development IMP
Inferred from Mutant Phenotype
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 positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in regulation of postsynapse organization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of postsynapse organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
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 trigeminal nerve structural organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within trunk neural crest cell migration 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
located_in extracellular region IEA
Inferred from Electronic Annotation
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-3F
Names
semaphorin IV

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)

  1. NM_001311151.3NP_001298080.1  semaphorin-3F isoform 1 precursor

    See identical proteins and their annotated locations for NP_001298080.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC152718, AC162905
    Consensus CDS
    CCDS81069.1
    UniProtKB/Swiss-Prot
    O88632, O88633
    Related
    ENSMUSP00000141865.2, ENSMUST00000192727.6
    Conserved Domains (3) summary
    cd05871
    Location:609697
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48548
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00423
    Location:547584
    PSI; domain found in Plexins, Semaphorins and Integrins
  2. NM_001379496.2NP_001366425.1  semaphorin-3F isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AC152718, AC162905
    Conserved Domains (3) summary
    cd11254
    Location:48517
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00423
    Location:516553
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:577666
    Ig_Sema3; Immunoglobulin (Ig)-like domain of class III semaphorin Sema3
  3. NM_001405023.1NP_001391952.1  semaphorin-3F isoform 4 precursor

    Status: VALIDATED

    Source sequence(s)
    AC152718, AC162905
  4. NM_001405024.1NP_001391953.1  semaphorin-3F isoform 5 precursor

    Status: VALIDATED

    Source sequence(s)
    AC152718, AC162905
  5. NM_001405025.2NP_001391954.1  semaphorin-3F isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AC152718, AC162905
    UniProtKB/Swiss-Prot
    O88633
  6. NM_011349.4NP_035479.2  semaphorin-3F isoform 2 precursor

    See identical proteins and their annotated locations for NP_035479.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AC152718, AC162905
    Consensus CDS
    CCDS23505.1
    UniProtKB/Swiss-Prot
    O88632
    Related
    ENSMUSP00000079400.4, ENSMUST00000080560.9
    Conserved Domains (3) summary
    cd11254
    Location:48517
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00423
    Location:516553
    PSI; domain found in Plexins, Semaphorins and Integrins
    cd05871
    Location:577666
    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_000075.7 Reference GRCm39 C57BL/6J

    Range
    107558698..107587674 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017313228.3XP_017168717.1  semaphorin-3F isoform X3

    UniProtKB/Swiss-Prot
    O88632
    Conserved Domains (3) summary
    cd05871
    Location:609697
    Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
    cd11254
    Location:48548
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00423
    Location:547584
    PSI; domain found in Plexins, Semaphorins and Integrins
  2. XM_017313230.2XP_017168719.1  semaphorin-3F isoform X4

    Conserved Domains (3) summary
    smart00423
    Location:321358
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:383424
    Ig; Immunoglobulin domain
    cl15693
    Location:1322
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  3. XM_017313229.3XP_017168718.1  semaphorin-3F isoform X4

    Conserved Domains (3) summary
    smart00423
    Location:321358
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:383424
    Ig; Immunoglobulin domain
    cl15693
    Location:1322
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  4. XM_017313227.3XP_017168716.1  semaphorin-3F isoform X2

    Conserved Domains (3) summary
    cd11254
    Location:48517
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00423
    Location:516553
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:578619
    Ig; Immunoglobulin domain
  5. XM_017313226.3XP_017168715.1  semaphorin-3F isoform X1

    Conserved Domains (3) summary
    cd11254
    Location:48548
    Sema_3F; The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F)
    smart00423
    Location:547584
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:609650
    Ig; Immunoglobulin domain

RNA

  1. XR_379758.5 RNA Sequence

  2. XR_871078.4 RNA Sequence

  3. XR_379759.5 RNA Sequence