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    SEMA4A semaphorin 4A [ Homo sapiens (human) ]

    Gene ID: 64218, updated on 15-Jun-2019

    Summary

    Official Symbol
    SEMA4Aprovided by HGNC
    Official Full Name
    semaphorin 4Aprovided by HGNC
    Primary source
    HGNC:HGNC:10729
    See related
    Ensembl:ENSG00000196189 MIM:607292
    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
    RP35; SEMB; SEMAB; CORD10
    Summary
    This gene encodes a member of the semaphorin family of soluble and transmembrane proteins. Semaphorins are involved in numerous functions, including axon guidance, morphogenesis, carcinogenesis, and immunomodulation. The encoded protein is a single-pass type I membrane protein containing an immunoglobulin-like C2-type domain, a PSI domain and a sema domain. It inhibits axonal extension by providing local signals to specify territories inaccessible for growing axons. It is an activator of T-cell-mediated immunity and suppresses vascular endothelial growth factor (VEGF)-mediated endothelial cell migration and proliferation in vitro and angiogenesis in vivo. Mutations in this gene are associated with retinal degenerative diseases including retinitis pigmentosa type 35 (RP35) and cone-rod dystrophy type 10 (CORD10). Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]
    Expression
    Broad expression in skin (RPKM 12.9), lymph node (RPKM 12.8) and 20 other tissues See more
    Orthologs

    Genomic context

    See SEMA4A in Genome Data Viewer
    Location:
    1q22
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (156149672..156177751)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156117145..156147542)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene mex-3 RNA binding family member A Neighboring gene lamin A/C Neighboring gene VISTA enhancer hs2129 Neighboring gene solute carrier family 25 member 44 Neighboring gene PMF1-BGLAP readthrough Neighboring gene polyamine modulated factor 1

    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?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of SEMA4A PubMed

    Go to the HIV-1, Human Interaction Database

    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...
    • Axon guidance, organism-specific biosystem (from REACTOME)
      Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • Other semaphorin interactions, organism-specific biosystem (from REACTOME)
      Other semaphorin interactions, organism-specific biosystemThere are eight classes of semaphorins and four types of plexins. Semaphorin (SEMA) classes 1 and 2 are found in invertebrates and classes 3-7 are vertebrate sempahorines. Sempahorin class 3 is secre...
    • Semaphorin interactions, organism-specific biosystem (from REACTOME)
      Semaphorin interactions, organism-specific biosystemSemaphorins are a large family of cell surface and secreted guidance molecules divided into eight classes on the basis of their structures. They all have an N-terminal conserved sema domain. Semaphor...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ12287

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    chemorepellent activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    neuropilin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    semaphorin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    T-helper 1 cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    axonogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    negative chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    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 
    positive regulation of excitatory synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of inhibitory synapse assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of cell shape IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of endothelial cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    semaphorin-plexin signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    cytosol IDA
    Inferred from Direct Assay
    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 
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
     
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

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

    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_027683.1 RefSeqGene

      Range
      5001..32808
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001193300.2NP_001180229.1  semaphorin-4A isoform 1 precursor

      See identical proteins and their annotated locations for NP_001180229.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, as compared to variant 1. Variants 1-3 encode the same isoform (1).
      Source sequence(s)
      AL135927
      Consensus CDS
      CCDS1132.1
      UniProtKB/Swiss-Prot
      Q9H3S1
      Conserved Domains (3) summary
      cd11256
      Location:55495
      Sema_4A; The Sema domain, a protein interacting module, of semaphorin 4A (Sema4A)
      pfam01437
      Location:496540
      PSI; Plexin repeat
      cl11960
      Location:566638
      Ig; Immunoglobulin domain
    2. NM_001193301.1NP_001180230.1  semaphorin-4A isoform 1 precursor

      See identical proteins and their annotated locations for NP_001180230.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has an alternate 5' UTR, as compared to variant 1. Variants 1-3 encode the same isoform (1).
      Source sequence(s)
      AA761091, AY358531, DC332598
      Consensus CDS
      CCDS1132.1
      UniProtKB/Swiss-Prot
      Q9H3S1
      Related
      ENSP00000347117.2, ENST00000355014.6
      Conserved Domains (3) summary
      cd11256
      Location:55495
      Sema_4A; The Sema domain, a protein interacting module, of semaphorin 4A (Sema4A)
      pfam01437
      Location:496540
      PSI; Plexin repeat
      cl11960
      Location:566638
      Ig; Immunoglobulin domain
    3. NM_001193302.1NP_001180231.1  semaphorin-4A isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two internal exons in 5' different regions respectively, resulting in a downstream AUG start codon, as compared to variant 1. The resulting isoform (2) is shorter at the N-terminus and lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      AA761091, AK091127, AY358531
      Consensus CDS
      CCDS53378.1
      UniProtKB/Swiss-Prot
      Q9H3S1
      Related
      ENSP00000357267.1, ENST00000368284.5
      Conserved Domains (3) summary
      pfam01437
      Location:364408
      PSI; Plexin repeat
      cl11960
      Location:434506
      Ig; Immunoglobulin domain
      cl15693
      Location:1363
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    4. NM_001370567.1NP_001357496.1  semaphorin-4A isoform 1 precursor

      Status: REVIEWED

      Source sequence(s)
      AL135927
    5. NM_001370568.1NP_001357497.1  semaphorin-4A isoform 3

      Status: REVIEWED

      Source sequence(s)
      AL135927
    6. NM_001370569.1NP_001357498.1  semaphorin-4A isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL135927
    7. NM_001370571.1NP_001357500.1  semaphorin-4A isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL135927
    8. NM_022367.4NP_071762.2  semaphorin-4A isoform 1 precursor

      See identical proteins and their annotated locations for NP_071762.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) is the longest transcript. Variants 1-3 encode the same isoform (1).
      Source sequence(s)
      AY358531, BC020974, DA409501
      Consensus CDS
      CCDS1132.1
      UniProtKB/Swiss-Prot
      Q9H3S1
      Related
      ENSP00000357268.3, ENST00000368285.8
      Conserved Domains (3) summary
      cd11256
      Location:55495
      Sema_4A; The Sema domain, a protein interacting module, of semaphorin 4A (Sema4A)
      pfam01437
      Location:496540
      PSI; Plexin repeat
      cl11960
      Location:566638
      Ig; Immunoglobulin domain

    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.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      156149672..156177751
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509871.3XP_011508173.1  semaphorin-4A isoform X1

      Conserved Domains (3) summary
      cd11256
      Location:17457
      Sema_4A; The Sema domain, a protein interacting module, of semaphorin 4A (Sema4A)
      pfam01437
      Location:458502
      PSI; Plexin repeat
      cl11960
      Location:528600
      Ig; Immunoglobulin domain
    2. XM_011509878.2XP_011508180.1  semaphorin-4A isoform X3

      See identical proteins and their annotated locations for XP_011508180.1

      UniProtKB/TrEMBL
      B4DKS5
      Conserved Domains (3) summary
      pfam01437
      Location:397441
      PSI; Plexin repeat
      cl11960
      Location:467539
      Ig; Immunoglobulin domain
      cl15693
      Location:1396
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    3. XM_011509872.2XP_011508174.1  semaphorin-4A isoform X2

      See identical proteins and their annotated locations for XP_011508174.1

      UniProtKB/Swiss-Prot
      Q9H3S1
      Conserved Domains (3) summary
      cd11256
      Location:55495
      Sema_4A; The Sema domain, a protein interacting module, of semaphorin 4A (Sema4A)
      pfam01437
      Location:496540
      PSI; Plexin repeat
      cl11960
      Location:566638
      Ig; Immunoglobulin domain
    4. XM_011509875.3XP_011508177.1  semaphorin-4A isoform X3

      See identical proteins and their annotated locations for XP_011508177.1

      UniProtKB/TrEMBL
      B4DKS5
      Conserved Domains (3) summary
      pfam01437
      Location:397441
      PSI; Plexin repeat
      cl11960
      Location:467539
      Ig; Immunoglobulin domain
      cl15693
      Location:1396
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
    5. XM_011509874.2XP_011508176.1  semaphorin-4A isoform X3

      See identical proteins and their annotated locations for XP_011508176.1

      UniProtKB/TrEMBL
      B4DKS5
      Conserved Domains (3) summary
      pfam01437
      Location:397441
      PSI; Plexin repeat
      cl11960
      Location:467539
      Ig; Immunoglobulin domain
      cl15693
      Location:1396
      Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
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