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Sema6a semaphorin 6A [ Rattus norvegicus (Norway rat) ]

Gene ID: 361324, updated on 11-Apr-2024

Summary

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Official Symbol
Sema6aprovided by RGD
Official Full Name
semaphorin 6Aprovided by RGD
Primary source
RGD:1305493
See related
Ensembl:ENSRNOG00000004033 AllianceGenome:RGD:1305493
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 identical protein binding activity; signaling receptor binding activity; and transmembrane signaling receptor activity. Predicted to be involved in several processes, including generation of neurons; negative regulation of cell adhesion involved in sprouting angiogenesis; and negative regulation of signal transduction. Predicted to act upstream of or within cell surface receptor signaling pathway and centrosome localization. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Orthologous to human SEMA6A (semaphorin 6A). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Lung (RPKM 118.1), Kidney (RPKM 79.3) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
18q11
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 18 NC_086036.1 (42237227..42358540, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 18 NC_051353.1 (40050623..40171954, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 18 NC_005117.4 (41330519..41451813, complement)

Chromosome 18 - NC_086036.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134482946 Neighboring gene uncharacterized LOC134482943 Neighboring gene uncharacterized LOC134482944 Neighboring gene uncharacterized LOC134482945 Neighboring gene cytochrome c oxidase subunit 6C-2-like Neighboring gene uncharacterized LOC134482947 Neighboring gene small nucleolar RNA SNORA48

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. Semaphorin 6A improves functional recovery in conjunction with motor training after cerebral ischemia. Rogalewski A, et al. PLoS One, 2010 May 20. PMID 20505770, Free PMC Article
  2. The transmembrane semaphorin Sema6A controls cerebellar granule cell migration. Kerjan G, et al. Nat Neurosci, 2005 Nov. PMID 16205717
  3. Structural basis for semaphorin signalling through the plexin receptor. Nogi T, et al. Nature, 2010 Oct 28. PMID 20881961
  4. Plexin-A2 and its ligand, Sema6A, control nucleus-centrosome coupling in migrating granule cells. Renaud J, et al. Nat Neurosci, 2008 Apr. PMID 18327254
  5. MicroRNA-27a/b controls endothelial cell repulsion and angiogenesis by targeting semaphorin 6A. Urbich C, et al. Blood, 2012 Feb 9. PMID 22184411

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Semaphorin 6a overexpressed in the cortex enhances recovery after cerebral ischemia.
    Title: Semaphorin 6A improves functional recovery in conjunction with motor training after cerebral ischemia.
Submit: New GeneRIF Correction

Pathways from PubChem

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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 identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables semaphorin receptor binding ISO
Inferred from Sequence Orthology
more info
  
enables transmembrane signaling receptor activity 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 ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within cell surface receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
  
involved_in cellular response to vascular endothelial growth factor stimulus ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within centrosome localization ISO
Inferred from Sequence Orthology
more info
  
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of ERK1 and ERK2 cascade ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of angiogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of cell adhesion involved in sprouting angiogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of sprouting angiogenesis ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of vascular endothelial growth factor signaling pathway ISO
Inferred from Sequence Orthology
more info
  
involved_in neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron migration ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of neuron migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of neuron migration ISO
Inferred from Sequence Orthology
more info
  
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in semaphorin-plexin signaling pathway ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
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
  

General protein information

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Preferred Names
semaphorin-6A
Names
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A
semaphorin 6A-1

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_001108430.3 → NP_001101900.2  semaphorin-6A isoform 1 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    JAXUCZ010000018
    UniProtKB/TrEMBL
    A6IWY3, D3ZAG0
    Related
    ENSRNOP00000005476.7, ENSRNOT00000005476.9
    Conserved Domains (2) summary
    cd11266
    Location:48 → 513
    Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
    pfam01437
    Location:514 → 544
    PSI; Plexin repeat

  2. NM_001372354.2 → NP_001359283.1  semaphorin-6A isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    JAXUCZ010000018
    UniProtKB/TrEMBL
    A0A8I5ZYF8
    Related
    ENSRNOP00000082708.1, ENSRNOT00000115179.1
    Conserved Domains (2) summary
    cd11266
    Location:48 → 513
    Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
    pfam01437
    Location:514 → 546
    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_086036.1 Reference GRCr8

    Range
    42237227..42358540 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063277473.1 → XP_063133543.1  semaphorin-6A isoform X3

  2. XM_039096967.2 → XP_038952895.1  semaphorin-6A isoform X1

    UniProtKB/TrEMBL
    D3ZAX7
    Conserved Domains (2) summary
    cd11266
    Location:48 → 513
    Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
    pfam01437
    Location:514 → 544
    PSI; Plexin repeat

  3. XM_003751782.6 → XP_003751830.1  semaphorin-6A isoform X1

    See identical proteins and their annotated locations for XP_003751830.1

    UniProtKB/TrEMBL
    D3ZAX7
    Related
    ENSRNOP00000005446.5
    Conserved Domains (2) summary
    cd11266
    Location:48 → 513
    Sema_6A; The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A)
    pfam01437
    Location:514 → 544
    PSI; Plexin repeat

  4. XM_063277472.1 → XP_063133542.1  semaphorin-6A isoform X2

    UniProtKB/TrEMBL
    A6IWY3, D3ZAG0
Nucleotide Protein Strain
Heading Accession and Version

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