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    Sema5b sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B [ Mus musculus (house mouse) ]

    Gene ID: 20357, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Sema5bprovided by MGI
    Official Full Name
    sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5Bprovided by MGI
    Primary source
    MGI:MGI:107555
    See related
    Ensembl:ENSMUSG00000052133 AllianceGenome:MGI:107555
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    SemG; Semag; mKIAA1445
    Summary
    Predicted to enable chemorepellent activity and semaphorin receptor binding activity. Acts upstream of or within axon extension; detection of light stimulus involved in visual perception; and neuron projection guidance. Predicted to be located in membrane. Predicted to be active in plasma membrane. Is expressed in several structures, including central nervous system; future brain; genitourinary system; and trunk connective tissue. Orthologous to human SEMA5B (semaphorin 5B). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in adrenal adult (RPKM 16.2), CNS E11.5 (RPKM 13.7) and 11 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Sema5b in Genome Data Viewer
    Location:
    16 B3; 16 25.37 cM
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 16 NC_000082.7 (35361517..35485103)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 16 NC_000082.6 (35541154..35664261)

    Chromosome 16 - NC_000082.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1600019K03 gene Neighboring gene PRAME family member 8 pseudogene Neighboring gene VISTA enhancer mm1471 Neighboring gene 40S ribosomal protein S21 pseudogene Neighboring gene solute carrier family 49 member 4 Neighboring gene predicted gene, 25967 Neighboring gene CapStarr-seq enhancer MGSCv37_chr16:35747524-35747731 Neighboring gene Hspb associated protein 1 Neighboring gene STARR-seq mESC enhancer starr_40745 Neighboring gene predicted gene, 26838

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Remote ischemic preconditioning causes transient cell cycle arrest and renal protection by a NF-κB-dependent Sema5B pathway. Rossaint J, et al. JCI Insight, 2022 Jul 22. PMID 35727636, Free PMC Article
    2. Identification of a novel transmembrane semaphorin expressed on lymphocytes. Furuyama T, et al. J Biol Chem, 1996 Dec 27. PMID 8969198
    3. Semaphorin 5A inhibits synaptogenesis in early postnatal- and adult-born hippocampal dentate granule cells. Duan Y, et al. Elife, 2014 Oct 14. PMID 25313870, Free PMC Article
    4. A novel class of murine semaphorins with homology to thrombospondin is differentially expressed during early embryogenesis. Adams RH, et al. Mech Dev, 1996 Jun. PMID 8817451
    5. The sensory innervation of the mouse spinal cord may be patterned by differential expression of and differential responsiveness to semaphorins. Püschel AW, et al. Mol Cell Neurosci, 1996 May. PMID 8812066

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Gene trapped (1) 
    • Targeted (3)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    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
    		  
    Process Evidence Code Pubs
    involved_in axon extension IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within axon extension IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    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 IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within neuron projection extension IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within neuron projection extension IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within neuron projection guidance IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within neuron projection guidance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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-5B
    Names
    sema G
    semaphorin-G

    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_013661.3 → NP_038689.2  semaphorin-5B precursor

      See identical proteins and their annotated locations for NP_038689.2

      Status: VALIDATED

      Source sequence(s)
      AC154653, CT010576
      Consensus CDS
      CCDS28140.1
      UniProtKB/Swiss-Prot
      B1B1A9, Q60519, Q6ZPQ8, Q7TT33, Q8BVE5
      Related
      ENSMUSP00000057494.9, ENSMUST00000050625.15
      Conserved Domains (4) summary
      smart00209
      Location:798 → 850
      TSP1; Thrombospondin type 1 repeats
      pfam01437
      Location:497 → 544
      PSI; Plexin repeat
      cl15278
      Location:911 → 952
      TSP_1; Thrombospondin type 1 domain
      cl15693
      Location:60 → 496
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000082.7 Reference GRCm39 C57BL/6J

      Range
      35361517..35485103
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006521869.2 → XP_006521932.1  semaphorin-5B isoform X1

      See identical proteins and their annotated locations for XP_006521932.1

      UniProtKB/Swiss-Prot
      Q60519
      Related
      ENSMUSP00000112536.2, ENSMUST00000120756.8
      Conserved Domains (4) summary
      smart00209
      Location:827 → 879
      TSP1; Thrombospondin type 1 repeats
      pfam01437
      Location:497 → 544
      PSI; Plexin repeat
      cl15278
      Location:940 → 981
      TSP_1; Thrombospondin type 1 domain
      cl15693
      Location:60 → 496
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    2. XM_011245844.1 → XP_011244146.1  semaphorin-5B isoform X1

      See identical proteins and their annotated locations for XP_011244146.1

      UniProtKB/Swiss-Prot
      Q60519
      Conserved Domains (4) summary
      smart00209
      Location:827 → 879
      TSP1; Thrombospondin type 1 repeats
      pfam01437
      Location:497 → 544
      PSI; Plexin repeat
      cl15278
      Location:940 → 981
      TSP_1; Thrombospondin type 1 domain
      cl15693
      Location:60 → 496
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    3. XM_030249006.1 → XP_030104866.1  semaphorin-5B isoform X2

      UniProtKB/Swiss-Prot
      B1B1A9, Q60519, Q6ZPQ8, Q7TT33, Q8BVE5
      Conserved Domains (4) summary
      smart00209
      Location:798 → 850
      TSP1; Thrombospondin type 1 repeats
      pfam01437
      Location:497 → 544
      PSI; Plexin repeat
      cl15278
      Location:911 → 952
      TSP_1; Thrombospondin type 1 domain
      cl15693
      Location:60 → 496
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

    RNA

    1. XR_004939173.1 RNA Sequence

    2. XR_875743.3 RNA Sequence

    3. XR_003951770.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q60519.2 GenPept UniProtKB/Swiss-Prot:Q60519

    Gene LinkOut

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

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