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SEMA4A semaphorin 4A [ Homo sapiens (human) ]

Gene ID: 64218, updated on 10-Dec-2024

Summary

Official Symbol
SEMA4Aprovided by HGNC
Official Full Name
semaphorin 4Aprovided by HGNC
Primary source
HGNC:HGNC:10729
See related
Ensembl:ENSG00000196189 MIM:607292; AllianceGenome:HGNC:10729
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
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Genomic context

See SEMA4A in Genome Data Viewer
Location:
1q22
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (156147373..156177744)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (155285786..155316193)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (156119735..156147535)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:156045982-156046889 and GRCh37_chr1:156046890-156047796 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156051244-156052056 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156052057-156052870 Neighboring gene mex-3 RNA binding family member A Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:156056191-156057025 Neighboring gene Sharpr-MPRA regulatory region 15377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1838 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156067261-156068134 Neighboring gene lamin A/C Neighboring gene VISTA enhancer hs2129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156077037-156077778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:156087275-156087774 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156090429-156091415 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156093390-156094377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1843 Neighboring gene Sharpr-MPRA regulatory region 4592 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1845 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156096352-156097337 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1846 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:156099693-156100892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1847 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1848 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1850 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:156131887-156132038 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156146693-156147195 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156149713-156150215 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:156151223-156151726 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:156151727-156152229 Neighboring gene uncharacterized LOC124900449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1853 Neighboring gene solute carrier family 25 member 44

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 Functions

What'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 PubChem

Interactions

General gene information

Clone Names

  • FLJ12287

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chemorepellent activity  
enables neuropilin binding  
enables protein binding PubMed 
enables semaphorin receptor binding  
Process Evidence Code Pubs
involved_in T-helper 1 cell differentiation  
involved_in angiogenesis  
involved_in axon guidance  
involved_in negative chemotaxis  
involved_in negative regulation of angiogenesis  
involved_in neural crest cell migration  
involved_in positive regulation of cell migration  
involved_in positive regulation of excitatory synapse assembly  
involved_in positive regulation of inhibitory synapse assembly  
involved_in regulation of cell shape  
involved_in regulation of endothelial cell migration  
involved_in semaphorin-plexin signaling pathway  
Component Evidence Code Pubs
is_active_in plasma membrane  
located_in plasma membrane  

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)

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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.

Genomic

  1. NG_027683.1 RefSeqGene

    Range
    8642..32801
    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
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
    Conserved Domains (3) summary
    cd11256
    Location:55495
    Sema_4A; The Sema domain, a protein interacting module, of semaphorin 4A (Sema4A)
    smart00423
    Location:496541
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:566638
    Ig; Immunoglobulin domain
  2. NM_001193301.2NP_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)
    AY358531
    Consensus CDS
    CCDS1132.1
    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
    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)
    smart00423
    Location:496541
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:566638
    Ig; Immunoglobulin domain
  3. NM_001193302.2NP_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)
    AK091127, AY358531
    Consensus CDS
    CCDS53378.1
    UniProtKB/TrEMBL
    Q5TCJ5
    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
    Consensus CDS
    CCDS1132.1
    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
    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)
    smart00423
    Location:496541
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:566638
    Ig; Immunoglobulin domain
  5. NM_001370568.1NP_001357497.1  semaphorin-4A isoform 3

    Status: REVIEWED

    Source sequence(s)
    AL135927
    UniProtKB/TrEMBL
    B4DKS5, Q5TCJ5
    Conserved Domains (3) summary
    smart00423
    Location:397442
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:467539
    Ig; Immunoglobulin domain
    cl15693
    Location:1396
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  6. NM_001370569.1NP_001357498.1  semaphorin-4A isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL135927
    UniProtKB/TrEMBL
    Q5TCJ5
    Conserved Domains (3) summary
    smart00423
    Location:327372
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:397469
    Ig; Immunoglobulin domain
    cl15693
    Location:1326
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  7. NM_001370571.1NP_001357500.1  semaphorin-4A isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL135927
    UniProtKB/TrEMBL
    Q5TCJ5
    Conserved Domains (3) summary
    smart00423
    Location:327372
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:397469
    Ig; Immunoglobulin domain
    cl15693
    Location:1326
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  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
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
    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)
    smart00423
    Location:496541
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:566638
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    156147373..156177744
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427664.1XP_047283620.1  semaphorin-4A isoform X2

    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
  2. XM_047427677.1XP_047283633.1  semaphorin-4A isoform X3

    UniProtKB/TrEMBL
    B4DKS5, Q5TCJ5
  3. XM_011509878.3XP_011508180.1  semaphorin-4A isoform X3

    See identical proteins and their annotated locations for XP_011508180.1

    UniProtKB/TrEMBL
    B4DKS5, Q5TCJ5
    Conserved Domains (3) summary
    smart00423
    Location:397442
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:467539
    Ig; Immunoglobulin domain
    cl15693
    Location:1396
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  4. XM_011509871.4XP_011508173.1  semaphorin-4A isoform X1

    UniProtKB/TrEMBL
    Q5TCJ5
    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
  5. XM_047427678.1XP_047283634.1  semaphorin-4A isoform X4

    Related
    ENST00000487358.5
  6. XM_047427670.1XP_047283626.1  semaphorin-4A isoform X2

    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
  7. XM_047427671.1XP_047283627.1  semaphorin-4A isoform X2

    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
  8. XM_011509872.3XP_011508174.1  semaphorin-4A isoform X2

    See identical proteins and their annotated locations for XP_011508174.1

    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
    Conserved Domains (3) summary
    cd11256
    Location:55495
    Sema_4A; The Sema domain, a protein interacting module, of semaphorin 4A (Sema4A)
    smart00423
    Location:496541
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:566638
    Ig; Immunoglobulin domain
  9. XM_011509874.3XP_011508176.1  semaphorin-4A isoform X3

    See identical proteins and their annotated locations for XP_011508176.1

    UniProtKB/TrEMBL
    B4DKS5, Q5TCJ5
    Conserved Domains (3) summary
    smart00423
    Location:397442
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:467539
    Ig; Immunoglobulin domain
    cl15693
    Location:1396
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  10. XM_011509875.4XP_011508177.1  semaphorin-4A isoform X3

    See identical proteins and their annotated locations for XP_011508177.1

    UniProtKB/TrEMBL
    B4DKS5, Q5TCJ5
    Conserved Domains (3) summary
    smart00423
    Location:397442
    PSI; domain found in Plexins, Semaphorins and Integrins
    cl11960
    Location:467539
    Ig; Immunoglobulin domain
    cl15693
    Location:1396
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    155285786..155316193
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338170.1XP_054194145.1  semaphorin-4A isoform X2

    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
  2. XM_054338167.1XP_054194142.1  semaphorin-4A isoform X5

    UniProtKB/TrEMBL
    Q5TCJ5
  3. XM_054338176.1XP_054194151.1  semaphorin-4A isoform X6

  4. XM_054338175.1XP_054194150.1  semaphorin-4A isoform X3

    UniProtKB/TrEMBL
    B4DKS5, Q5TCJ5
  5. XM_054338171.1XP_054194146.1  semaphorin-4A isoform X2

    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
  6. XM_054338172.1XP_054194147.1  semaphorin-4A isoform X2

    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
  7. XM_054338168.1XP_054194143.1  semaphorin-4A isoform X2

    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
  8. XM_054338169.1XP_054194144.1  semaphorin-4A isoform X2

    UniProtKB/Swiss-Prot
    B2RDH8, B3KR76, Q5TCI5, Q5TCJ6, Q8WUA9, Q9H3S1
    UniProtKB/TrEMBL
    Q5TCJ5
  9. XM_054338173.1XP_054194148.1  semaphorin-4A isoform X3

    UniProtKB/TrEMBL
    B4DKS5, Q5TCJ5
  10. XM_054338174.1XP_054194149.1  semaphorin-4A isoform X3

    UniProtKB/TrEMBL
    B4DKS5, Q5TCJ5
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