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Sema4b semaphorin 4B [ Rattus norvegicus (Norway rat) ]

Gene ID: 293042, updated on 11-Apr-2024

Summary

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Official Symbol
Sema4bprovided by RGD
Official Full Name
semaphorin 4Bprovided by RGD
Primary source
RGD:1307872
See related
Ensembl:ENSRNOG00000025167 AllianceGenome:RGD:1307872
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 generation of neurons; neural crest cell migration; and semaphorin-plexin signaling pathway. Predicted to be located in plasma membrane and synapse. Predicted to be active in extracellular space. Predicted to be integral component of plasma membrane. Orthologous to human SEMA4B (semaphorin 4B). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Spleen (RPKM 183.1), Kidney (RPKM 104.5) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
1q31
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (143545727..143587037)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (134136646..134177777)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (141986145..142014400)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102548889 Neighboring gene uncharacterized LOC134483744 Neighboring gene calcium and integrin binding 1 Neighboring gene GDP-D-glucose phosphorylase 1 Neighboring gene tubulin tyrosine ligase like 13

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 4B interacts with the post-synaptic density protein PSD-95/SAP90 and is recruited to synapses through a C-terminal PDZ-binding motif. Burkhardt C, et al. FEBS Lett, 2005 Jul 4. PMID 15978582
  2. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  4. 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 negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
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
is_active_in glutamatergic synapse ISO
Inferred from Sequence Orthology
more info
  
located_in membrane ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
  
located_in synapse ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
semaphorin-4B
Names
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B

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_001170462.2 → NP_001163933.1  semaphorin-4B precursor

    See identical proteins and their annotated locations for NP_001163933.1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000001
    UniProtKB/TrEMBL
    A0A8I6AWC2, A6JC85, F1LSV0
    Related
    ENSRNOP00000030864.6, ENSRNOT00000030914.7
    Conserved Domains (3) summary
    pfam01437
    Location:510 → 556
    PSI; Plexin repeat
    cd05872
    Location:577 → 661
    Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B
    cl15693
    Location:46 → 509
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

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_086019.1 Reference GRCr8

    Range
    143545727..143587037
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039105603.2 → XP_038961531.1  semaphorin-4B isoform X1

    UniProtKB/TrEMBL
    A0A8I6AWC2, A6JC85, F1LSV0
    Conserved Domains (3) summary
    pfam01437
    Location:510 → 556
    PSI; Plexin repeat
    cd05872
    Location:577 → 661
    Ig_Sema4B_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B
    cl15693
    Location:46 → 509
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  2. XM_039105606.2 → XP_038961534.1  semaphorin-4B isoform X2

    Conserved Domains (2) summary
    smart00423
    Location:510 → 534
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl15693
    Location:46 → 509
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
Nucleotide Protein Strain
Heading Accession and Version

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