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

    Gene ID: 29745, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Sema4fprovided by RGD
    Official Full Name
    ssemaphorin 4Fprovided by RGD
    Primary source
    RGD:3658
    See related
    EnsemblRapid: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; neuropilin binding 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 active in glutamatergic synapse and postsynaptic density membrane. Orthologous to human SEMA4F (ssemaphorin 4F). [provided by Alliance of Genome Resources, Dec 2024]
    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 neuropilin binding 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, ENSRNOT00000009269.6
      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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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