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Sema6b semaphorin 6B [ Rattus norvegicus (Norway rat) ]

Gene ID: 84609, updated on 2-May-2024

Summary

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Official Symbol
Sema6bprovided by RGD
Official Full Name
semaphorin 6Bprovided by RGD
Primary source
RGD:69278
See related
Ensembl:ENSRNOG00000045998 AllianceGenome:RGD:69278
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 nervous system development; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Human ortholog(s) of this gene implicated in progressive myoclonus epilepsy. Orthologous to human SEMA6B (semaphorin 6B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Brain (RPKM 54.3), Spleen (RPKM 15.9) and 6 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Sema6b in Genome Data Viewer
Location:
9q11
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (1038103..1055063, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (950939..967905, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (10934273..10951252)

Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene perilipin 5 Neighboring gene leucine-rich alpha-2-glycoprotein 1 Neighboring gene TNF alpha induced protein 8 like 1 Neighboring gene uncharacterized LOC134480469 Neighboring gene myeloid-derived growth factor Neighboring gene dipeptidyl peptidase 9

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. Molecular cloning of a novel member of semaphorin family genes, semaphorin Z. Kikuchi K, et al. Brain Res Mol Brain Res, 1997 Nov. PMID 9427525
  2. Plexin-a4 mediates axon-repulsive activities of both secreted and transmembrane semaphorins and plays roles in nerve fiber guidance. Suto F, et al. J Neurosci, 2005 Apr 6. PMID 15814794, 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
  
enables semaphorin receptor binding IEA
Inferred from Electronic Annotation
more info
  
enables semaphorin receptor binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in axon guidance IEA
Inferred from Electronic Annotation
more info
  
involved_in axon guidance ISO
Inferred from Sequence Orthology
more info
  
involved_in axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in central nervous system development ISO
Inferred from Sequence Orthology
more info
  
involved_in central nervous system development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in hippocampus development IEA
Inferred from Electronic Annotation
more info
  
involved_in hippocampus development ISO
Inferred from Sequence Orthology
more info
  
involved_in hippocampus development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
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
  
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
semaphorin-6B
Names
sema Z
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B
semaphorin-Z

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_053471.4 → NP_445923.1  semaphorin-6B precursor

    See identical proteins and their annotated locations for NP_445923.1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000009
    UniProtKB/Swiss-Prot
    O70141
    UniProtKB/TrEMBL
    A0A8L2QYG3
    Related
    ENSRNOP00000067668.2, ENSRNOT00000070794.2
    Conserved Domains (3) summary
    cd11267
    Location:58 → 526
    Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
    PHA03247
    Location:698 → 885
    PHA03247; large tegument protein UL36; Provisional
    pfam01437
    Location:527 → 556
    PSI; Plexin repeat

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_086027.1 Reference GRCr8

    Range
    1038103..1055063 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006244349.5 → XP_006244411.1  semaphorin-6B isoform X2

    See identical proteins and their annotated locations for XP_006244411.1

    UniProtKB/Swiss-Prot
    O70141
    UniProtKB/TrEMBL
    A0A8L2QYG3
    Conserved Domains (3) summary
    cd11267
    Location:58 → 526
    Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
    PHA03247
    Location:698 → 885
    PHA03247; large tegument protein UL36; Provisional
    pfam01437
    Location:527 → 556
    PSI; Plexin repeat

  2. XM_006244348.5 → XP_006244410.1  semaphorin-6B isoform X1

    UniProtKB/TrEMBL
    A0A8I5ZKZ1, A6KQZ7
    Related
    ENSRNOP00000078468.1
    Conserved Domains (2) summary
    cd11267
    Location:128 → 596
    Sema_6B; The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B)
    pfam01437
    Location:597 → 626
    PSI; Plexin repeat
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O70141.1 GenPept UniProtKB/Swiss-Prot:O70141

Gene LinkOut

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