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SEMA4A semaphorin 4A [ Homo sapiens (human) ]

Gene ID: 64218, updated on 13-Feb-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_001193300.1NP_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) has an alternate splice site in the 5' UTR, resulting in a shorter 5' UTR, as compared to variant 1. Variants 1-3 encode the same isoform (1).
    Source sequence(s)
    AA761091, AK315547, AY358531, DA508826
    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_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, ENST00000368285.7
    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.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 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_011509876.2XP_011508178.1  semaphorin-4A isoform X3

    See identical proteins and their annotated locations for XP_011508178.1

    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
  4. XM_011509879.2XP_011508181.1  semaphorin-4A isoform X4

    Conserved Domains (3) summary
    pfam01437
    Location:327371
    PSI; Plexin repeat
    cl11960
    Location:397469
    Ig; Immunoglobulin domain
    cl15693
    Location:1326
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  5. XM_017002057.1XP_016857546.1  semaphorin-4A isoform X4

    Conserved Domains (3) summary
    pfam01437
    Location:327371
    PSI; Plexin repeat
    cl11960
    Location:397469
    Ig; Immunoglobulin domain
    cl15693
    Location:1326
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  6. 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
  7. XM_011509873.2XP_011508175.1  semaphorin-4A isoform X2

    See identical proteins and their annotated locations for XP_011508175.1

    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
  8. 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
  9. 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
  10. XM_017002056.1XP_016857545.1  semaphorin-4A isoform X2

    UniProtKB/Swiss-Prot
    Q9H3S1
    Related
    ENSP00000357265.1, ENST00000368282.1
    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
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