U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Sema5b semaphorin 5B [ Rattus norvegicus (Norway rat) ]

    Gene ID: 303901, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Sema5bprovided by RGD
    Official Full Name
    semaphorin 5Bprovided by RGD
    Primary source
    RGD:1308914
    See related
    EnsemblRapid:ENSRNOG00000002238 AllianceGenome:RGD:1308914
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    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. Predicted to be involved in several processes, including axonogenesis; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to act upstream of or within detection of light stimulus involved in visual perception; neuron projection extension; and neuron projection guidance. Predicted to be active in plasma membrane. Orthologous to human SEMA5B (semaphorin 5B). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 41.8), Testes (RPKM 40.8) and 6 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Sema5b in Genome Data Viewer
    Location:
    11q22
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (78607805..78730724, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (65102532..65225456, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (68304844..68435109, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108352343 Neighboring gene solute carrier family 49 member 4 Neighboring gene metastasis associated 1 family, member 2, pseudogene 1 Neighboring gene uncharacterized LOC120095662 Neighboring gene protein disulfide isomerase family A, member 5 Neighboring gene uncharacterized LOC120095661

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Class 5 transmembrane semaphorins control selective Mammalian retinal lamination and function. Matsuoka RL, et al. Neuron, 2011 Aug 11. PMID 21835343, Free PMC Article
    2. 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

    Go to the top of the page Help

    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 extension IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within axon extension ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within detection of light stimulus involved in visual perception ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative chemotaxis 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within neuron projection guidance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of plasma membrane bounded cell projection organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    semaphorin-5B
    Names
    sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_001415135.1 → NP_001402064.1  semaphorin-5B precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000011
      UniProtKB/TrEMBL
      A6IRF8
      Related
      ENSRNOP00000091837.1, ENSRNOT00000095740.2

    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_086029.1 Reference GRCr8

      Range
      78607805..78730724 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039088340.2 → XP_038944268.1  semaphorin-5B isoform X1

      UniProtKB/TrEMBL
      A6IRF7
      Conserved Domains (3) summary
      smart00209
      Location:609 → 662
      TSP1; Thrombospondin type 1 repeats
      pfam01437
      Location:497 → 544
      PSI; Plexin repeat
      cl15693
      Location:60 → 496
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. XM_039088341.2 → XP_038944269.1  semaphorin-5B isoform X2

      Conserved Domains (3) summary
      smart00209
      Location:555 → 613
      TSP1; Thrombospondin type 1 repeats
      pfam01437
      Location:497 → 544
      PSI; Plexin repeat
      cl15693
      Location:60 → 496
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools