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SEMA4D semaphorin 4D [ Homo sapiens (human) ]

Gene ID: 10507, updated on 2-Aug-2020

Summary

Official Symbol
SEMA4Dprovided by HGNC
Official Full Name
semaphorin 4Dprovided by HGNC
Primary source
HGNC:HGNC:10732
See related
Ensembl:ENSG00000187764 MIM:601866
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
A8; GR3; BB18; CD100; COLL4; SEMAJ; coll-4; C9orf164; M-sema-G
Expression
Broad expression in lymph node (RPKM 12.0), appendix (RPKM 8.6) and 22 other tissues See more
Orthologs

Genomic context

See SEMA4D in Genome Data Viewer
Location:
9q22.2
Exon count:
30
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (89360787..89498113, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (91975706..92112906, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376136 Neighboring gene microRNA 3153 Neighboring gene SECIS binding protein 2 Neighboring gene CDC28 protein kinase regulatory subunit 2 Neighboring gene ubiquitin-conjugating enzyme E2 variant 1 pseudogene Neighboring gene proliferation-associated 2G4 pseudogene 6 Neighboring gene uncharacterized LOC105376137 Neighboring gene uncharacterized LOC105376139

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?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of SEMA4D PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of semaphoring-4D (SEMA4D) in human B cells PubMed
Nef nef Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD100 PubMed
Tat tat Microarray analysis indicates HIV-1 Tat upregulates the expression of many proteins, including Semaphorin (CD100), in immature dendritic cells, an effect that likely facilitates the expansion of HIV-1 infection PubMed
Vpu vpu Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD100 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ33485, FLJ34282, FLJ39737, FLJ46484, MGC169138, MGC169141

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chemorepellent activity 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 
semaphorin receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
semaphorin receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
 
signaling receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
signaling receptor binding IDA
Inferred from Direct Assay
more info
PubMed 
transmembrane signaling receptor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell adhesion TAS
Traceable Author Statement
more info
PubMed 
immune response TAS
Traceable Author Statement
more info
PubMed 
leukocyte aggregation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of alkaline phosphatase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of alkaline phosphatase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of apoptotic process TAS
Traceable Author Statement
more info
PubMed 
negative regulation of axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of osteoblast differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of peptidyl-tyrosine phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ossification involved in bone maturation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ossification involved in bone maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of GTPase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of GTPase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of collateral sprouting IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of inhibitory synapse assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of peptidyl-tyrosine phosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of phosphatidylinositol 3-kinase signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of cell projection organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cell shape IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of dendrite morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
semaphorin-plexin signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
semaphorin-plexin signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space ISS
Inferred from Sequence or Structural Similarity
more info
 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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

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.

mRNA and Protein(s)

  1. NM_001142287.2NP_001135759.1  semaphorin-4D isoform 2 precursor

    See identical proteins and their annotated locations for NP_001135759.1

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
    Consensus CDS
    CCDS47991.1
    UniProtKB/Swiss-Prot
    Q92854
    Related
    ENSP00000391733.1, ENST00000420987.5
    Conserved Domains (3) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503554
    PSI; Plexin repeat
    cl11960
    Location:600679
    Ig; Immunoglobulin domain
  2. NM_001371194.2NP_001358123.1  semaphorin-4D isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
    Related
    ENSP00000388768.2, ENST00000422704.6
  3. NM_001371195.1NP_001358124.1  semaphorin-4D isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  4. NM_001371196.1NP_001358125.1  semaphorin-4D isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  5. NM_001371197.1NP_001358126.1  semaphorin-4D isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  6. NM_001371198.1NP_001358127.1  semaphorin-4D isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  7. NM_001371199.1NP_001358128.1  semaphorin-4D isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
    Related
    ENSP00000344923.4, ENST00000339861.8
  8. NM_001371200.1NP_001358129.1  semaphorin-4D isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  9. NM_001371201.1NP_001358130.1  semaphorin-4D isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  10. NM_001371202.1NP_001358131.1  semaphorin-4D isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  11. NM_006378.4NP_006369.3  semaphorin-4D isoform 1 precursor

    See identical proteins and their annotated locations for NP_006369.3

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
    Consensus CDS
    CCDS6685.1
    UniProtKB/Swiss-Prot
    Q92854
    Related
    ENSP00000405102.2, ENST00000438547.6
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat

RNA

  1. NR_163884.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  2. NR_163885.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  3. NR_163886.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  4. NR_163887.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  5. NR_163888.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575
  6. NR_163889.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL590233, AL929575

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    89360787..89498113 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518133.2XP_011516435.1  semaphorin-4D isoform X1

    See identical proteins and their annotated locations for XP_011516435.1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  2. XM_011518125.1XP_011516427.1  semaphorin-4D isoform X1

    See identical proteins and their annotated locations for XP_011516427.1

    UniProtKB/Swiss-Prot
    Q92854
    Related
    ENSP00000348822.2, ENST00000356444.6
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  3. XM_011518128.2XP_011516430.1  semaphorin-4D isoform X1

    See identical proteins and their annotated locations for XP_011516430.1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  4. XM_011518127.2XP_011516429.1  semaphorin-4D isoform X1

    See identical proteins and their annotated locations for XP_011516429.1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  5. XM_011518123.2XP_011516425.1  semaphorin-4D isoform X1

    See identical proteins and their annotated locations for XP_011516425.1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  6. XM_011518129.1XP_011516431.1  semaphorin-4D isoform X1

    See identical proteins and their annotated locations for XP_011516431.1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  7. XM_017014198.1XP_016869687.1  semaphorin-4D isoform X1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  8. XM_017014195.1XP_016869684.1  semaphorin-4D isoform X1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  9. XM_017014194.1XP_016869683.1  semaphorin-4D isoform X1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  10. XM_011518124.2XP_011516426.1  semaphorin-4D isoform X1

    See identical proteins and their annotated locations for XP_011516426.1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  11. XM_017014193.2XP_016869682.1  semaphorin-4D isoform X1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  12. XM_011518131.2XP_011516433.1  semaphorin-4D isoform X1

    See identical proteins and their annotated locations for XP_011516433.1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  13. XM_011518130.2XP_011516432.1  semaphorin-4D isoform X1

    See identical proteins and their annotated locations for XP_011516432.1

    UniProtKB/Swiss-Prot
    Q92854
    Related
    ENSP00000416523.1, ENST00000450295.5
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  14. XM_011518134.2XP_011516436.1  semaphorin-4D isoform X1

    See identical proteins and their annotated locations for XP_011516436.1

    UniProtKB/Swiss-Prot
    Q92854
    Conserved Domains (4) summary
    cd05873
    Location:559645
    Ig_Sema4D_like; Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4D
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    smart00410
    Location:569634
    IG_like; Immunoglobulin like
    pfam01437
    Location:503554
    PSI; Plexin repeat
  15. XM_017014199.1XP_016869688.1  semaphorin-4D isoform X2

    Related
    ENSP00000446394.1, ENST00000537934.5
    Conserved Domains (1) summary
    cd11259
    Location:31485
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)

RNA

  1. XR_001746153.1 RNA Sequence

  2. XR_001746156.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_182635.1: Suppressed sequence

    Description
    NM_182635.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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