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Sema4f ssemaphorin 4F [ Rattus norvegicus (Norway rat) ]

Gene ID: 29745, updated on 13-Apr-2024

Summary

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Official Symbol
Sema4fprovided by RGD
Official Full Name
ssemaphorin 4Fprovided by RGD
Primary source
RGD:3658
See related
Ensembl:ENSRNOG00000006784 AllianceGenome:RGD:3658
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Involved in axon guidance. Acts upstream of or within negative regulation of axon extension and retinal ganglion cell axon guidance. Located in postsynaptic membrane. Is integral component of membrane. Orthologous to human SEMA4F (ssemaphorin 4F). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Brain (RPKM 36.9), Lung (RPKM 32.4) and 5 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Sema4f in Genome Data Viewer
Location:
4q34
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 4 NC_086022.1 (116969137..116995442, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 4 NC_051339.1 (115411411..115437721, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 4 NC_005103.4 (113738225..113764532, complement)

Chromosome 4 - NC_086022.1Genomic Context describing neighboring genes Neighboring gene hexokinase 2 Neighboring gene ribosomal protein S27a, pseudogene 18 Neighboring gene meiosis 1 associated protein Neighboring gene ribosomal protein S25, pseudogene 8 Neighboring gene small ribosomal subunit protein eS6-like

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Semaphorin4F interacts with the synapse-associated protein SAP90/PSD-95. Schultze W, et al. J Neurochem, 2001 Aug. PMID 11483650
  2. Cloning, expression, and genetic mapping of Sema W, a member of the semaphorin family. Encinas JA, et al. Proc Natl Acad Sci U S A, 1999 Mar 2. PMID 10051670, Free PMC Article
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

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 axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in axon guidance IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within negative regulation of axon extension IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
acts_upstream_of_or_within retinal ganglion cell axon guidance IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in dendrite IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
  
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 
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perikaryon IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in postsynaptic density membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in postsynaptic density membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in postsynaptic membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in synapse IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
semaphorin-4F
Names
Sema W
sema domain, immunoglobulin domain (Ig), TM domain, and short cy
sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F
semaphorin 4f
semaphorin-W

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_019272.2 → NP_062145.1  semaphorin-4F precursor

    See identical proteins and their annotated locations for NP_062145.1

    Status: PROVISIONAL

    Source sequence(s)
    JAXUCZ010000004
    UniProtKB/Swiss-Prot
    Q9Z143
    UniProtKB/TrEMBL
    A6IAI3
    Related
    ENSRNOP00000009269.4, ENSRNOT00000009269.5
    Conserved Domains (3) summary
    cd11261
    Location:57 → 516
    Sema_4F; The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F)
    pfam01437
    Location:517 → 568
    PSI; Plexin repeat
    cl11960
    Location:575 → 654
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086022.1 Reference GRCr8

    Range
    116969137..116995442 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039107372.2 → XP_038963300.1  semaphorin-4F isoform X1

    Conserved Domains (4) summary
    pfam01437
    Location:238 → 289
    PSI; Plexin repeat
    cd00096
    Location:296 → 301
    Ig; Ig strand A [structural motif]
    cl11960
    Location:296 → 375
    Ig; Immunoglobulin domain
    cl15693
    Location:55 → 237
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Z143.1 GenPept UniProtKB/Swiss-Prot:Q9Z143

Gene LinkOut

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