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    SEMA3B semaphorin 3B [ Homo sapiens (human) ]

    Gene ID: 7869, updated on 8-Dec-2018

    Summary

    Official Symbol
    SEMA3Bprovided by HGNC
    Official Full Name
    semaphorin 3Bprovided by HGNC
    Primary source
    HGNC:HGNC:10724
    See related
    Ensembl:ENSG00000012171 MIM:601281
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SemA; SEMA5; SEMAA; semaV; LUCA-1
    Summary
    The protein encoded by this gene belongs to the class-3 semaphorin/collapsin family, whose members function in growth cone guidance during neuronal development. This family member inhibits axonal extension and has been shown to act as a tumor suppressor by inducing apoptosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2014]
    Expression
    Broad expression in placenta (RPKM 31.6), small intestine (RPKM 29.6) and 20 other tissues See more
    Orthologs

    Genomic context

    See SEMA3B in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (50267558..50277171)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (50305040..50314573)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene microRNA 5787 Neighboring gene G protein subunit alpha i2 Neighboring gene SEMA3B antisense RNA 1 (head to head) Neighboring gene microRNA 6872 Neighboring gene leucine rich single-pass membrane protein 2 Neighboring gene interferon related developmental regulator 2 Neighboring gene hyaluronidase 3 Neighboring gene N(alpha)-acetyltransferase 80, NatH catalytic subunit

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    • Axon guidance, organism-specific biosystem (from KEGG)
      Axon guidance, organism-specific biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...
    • Axon guidance, conserved biosystem (from KEGG)
      Axon guidance, conserved biosystemAxon guidance represents a key stage in the formation of neuronal network. Axons are guided by a variety of guidance factors, such as netrins, ephrins, Slits, and semaphorins. These guidance cues are...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ34863

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    chemorepellent activity TAS
    Traceable Author Statement
    more info
    PubMed 
    neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    axon guidance TAS
    Traceable Author Statement
    more info
    PubMed 
    cell-cell signaling TAS
    Traceable Author Statement
    more info
    PubMed 
    chemorepulsion of axon TAS
    Traceable Author Statement
    more info
    PubMed 
    negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of axon extension involved in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    neural crest cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    semaphorin-3B
    Names
    sema A(V)
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B
    semaphorin A
    semaphorin-V

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_032938.1 RefSeqGene

      Range
      4951..14564
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001005914.2NP_001005914.1  semaphorin-3B isoform 2 precursor

      See identical proteins and their annotated locations for NP_001005914.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (2) that is 1 aa shorter than isoform 1. The 5' terminal exon of this variant is inferred based on tiled partial transcript alignments.
      Source sequence(s)
      AI309508, BC009113, BC013975, HY146744
      Consensus CDS
      CCDS77744.1
      UniProtKB/Swiss-Prot
      Q13214
      Related
      ENSP00000485281.1, ENST00000433753.4
      Conserved Domains (3) summary
      cd05871
      Location:574664
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      smart00423
      Location:514550
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl15693
      Location:46515
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    2. NM_001290060.1NP_001276989.1  semaphorin-3B isoform 1 precursor

      See identical proteins and their annotated locations for NP_001276989.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode isoform 1.
      Source sequence(s)
      AI309508, BC009113, HY152168, U28369
      Consensus CDS
      CCDS74941.1
      UniProtKB/Swiss-Prot
      Q13214
      Related
      ENSP00000484146.1, ENST00000616701.4
      Conserved Domains (3) summary
      cd05871
      Location:575665
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11250
      Location:46516
      Sema_3B; The Sema domain, a protein interacting module, of semaphorin 3B (Sema3B)
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins
    3. NM_001290061.1NP_001276990.1  semaphorin-3B isoform 3 precursor

      See identical proteins and their annotated locations for NP_001276990.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (3) is longer than isoform 1.
      Source sequence(s)
      AB083186, AI309508, BC009113, HY146744
      Consensus CDS
      CCDS77743.1
      UniProtKB/Swiss-Prot
      Q13214
      UniProtKB/TrEMBL
      A0A0C4DGV8
      Related
      ENSP00000480680.1, ENST00000611067.4
      Conserved Domains (3) summary
      cd05871
      Location:580670
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      smart00423
      Location:520556
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl15693
      Location:46521
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    4. NM_001290062.1NP_001276991.1  semaphorin-3B isoform 4

      See identical proteins and their annotated locations for NP_001276991.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several 5' exons but contains alternate 5' exon structure, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1. Both variants 5 and 6 encode isoform 4.
      Source sequence(s)
      AI309508, AK293678, BC009113, BC044602, DC330072
      Consensus CDS
      CCDS77745.1
      UniProtKB/Swiss-Prot
      Q13214
      UniProtKB/TrEMBL
      B4DEK9, Q6PI51
      Related
      ENSP00000485646.1, ENST00000456560.6
      Conserved Domains (3) summary
      smart00423
      Location:172208
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:232322
      Ig; Immunoglobulin domain
      cl15693
      Location:1173
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    5. NM_001290063.1NP_001276992.1  semaphorin-3B isoform 4

      See identical proteins and their annotated locations for NP_001276992.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks several 5' exons but contains alternate 5' exon structure, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter at the N-terminus, compared to isoform 1. Both variants 5 and 6 encode isoform 4.
      Source sequence(s)
      AI309508, AK293678, BC009113, DC330072
      Consensus CDS
      CCDS77745.1
      UniProtKB/Swiss-Prot
      Q13214
      UniProtKB/TrEMBL
      B4DEK9
      Related
      ENSP00000485173.1, ENST00000418576.3
      Conserved Domains (3) summary
      smart00423
      Location:172208
      PSI; domain found in Plexins, Semaphorins and Integrins
      cl11960
      Location:232322
      Ig; Immunoglobulin domain
      cl15693
      Location:1173
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    6. NM_004636.3NP_004627.1  semaphorin-3B isoform 1 precursor

      See identical proteins and their annotated locations for NP_004627.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1. Both variants 1 and 3 encode isoform 1. The 5' terminal exon of this variant is inferred based on tiled partial transcript alignments.
      Source sequence(s)
      AI309508, BC009113, HY146744, U28369
      Consensus CDS
      CCDS74941.1
      UniProtKB/Swiss-Prot
      Q13214
      Related
      ENSP00000481957.1, ENST00000618865.4
      Conserved Domains (3) summary
      cd05871
      Location:575665
      Ig_Semaphorin_classIII; Immunoglobulin (Ig)-like domain of class III semaphorin
      cd11250
      Location:46516
      Sema_3B; The Sema domain, a protein interacting module, of semaphorin 3B (Sema3B)
      smart00423
      Location:515551
      PSI; domain found in Plexins, Semaphorins and Integrins

    RNA

    1. NR_110697.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks several 5' exons but contains alternate 5' exon structure, and it also lacks three internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI309508, AK092182, BC009113, DC330072
      Related
      ENST00000456210.5

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

      Range
      50267558..50277171
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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