U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Sema4d sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [ Mus musculus (house mouse) ]

Gene ID: 20354, updated on 2-Apr-2024

Summary

Official Symbol
Sema4dprovided by MGI
Official Full Name
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4Dprovided by MGI
Primary source
MGI:MGI:109244
See related
Ensembl:ENSMUSG00000021451 AllianceGenome:MGI:109244
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
CD100; Semaj; Semcl2; coll-4; Semacl2
Summary
Enables semaphorin receptor binding activity. Involved in several processes, including negative regulation of osteoblast differentiation; positive regulation of inhibitory synapse assembly; and regulation of phosphate metabolic process. Acts upstream of or within positive regulation of axonogenesis. Located in extracellular space. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; hemolymphoid system; and respiratory system. Orthologous to human SEMA4D (semaphorin 4D). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in thymus adult (RPKM 32.3), spleen adult (RPKM 22.4) and 23 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See Sema4d in Genome Data Viewer
Location:
13 A5; 13 26.16 cM
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 13 NC_000079.7 (51839565..51947823, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 13 NC_000079.6 (51685529..51793678, complement)

Chromosome 13 - NC_000079.7Genomic Context describing neighboring genes Neighboring gene SECIS binding protein 2 Neighboring gene predicted gene, 22806 Neighboring gene CDC28 protein kinase regulatory subunit 2 Neighboring gene STARR-seq mESC enhancer starr_34521 Neighboring gene STARR-positive B cell enhancer ABC_E11544 Neighboring gene STARR-positive B cell enhancer ABC_E4068 Neighboring gene CapStarr-seq enhancer MGSCv37_chr13:51862969-51863152 Neighboring gene predicted gene, 19281 Neighboring gene CapStarr-seq enhancer MGSCv37_chr13:51896377-51896617 Neighboring gene CapStarr-seq enhancer MGSCv37_chr13:51909396-51909586 Neighboring gene CapStarr-seq enhancer MGSCv37_chr13:51941838-51941947 Neighboring gene growth arrest and DNA-damage-inducible 45 gamma Neighboring gene VISTA enhancer mm1565 Neighboring gene STARR-seq mESC enhancer starr_34529 Neighboring gene STARR-seq mESC enhancer starr_34531 Neighboring gene predicted gene, 26651

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables receptor ligand activity IDA
Inferred from Direct Assay
more info
PubMed 
enables semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables semaphorin receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables semaphorin receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables signaling receptor activity ISO
Inferred from Sequence Orthology
more info
 
enables signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables signaling receptor binding ISO
Inferred from Sequence Orthology
more info
 
enables transmembrane signaling receptor activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of axonogenesis IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of axonogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in bone trabecula morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in leukocyte aggregation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of cell adhesion ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of osteoblast differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of peptidyl-tyrosine phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within nervous system development IEA
Inferred from Electronic Annotation
more info
 
involved_in neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in ossification involved in bone maturation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in ossification involved in bone maturation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in ossification involved in bone maturation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of GTPase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of GTPase activity ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of Rho protein signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of axonogenesis IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within positive regulation of axonogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of cell migration ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of collateral sprouting ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of inhibitory synapse assembly IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of inhibitory synapse assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of peptidyl-tyrosine phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of protein phosphorylation ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of cell projection organization ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of cell shape ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of dendrite morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in semaphorin-plexin signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in semaphorin-plexin signaling pathway ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane TAS
Traceable Author Statement
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
 
part_of semaphorin receptor complex IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

Preferred Names
semaphorin-4D
Names
M-sema G
sema J
semaphorin H
semaphorin-C-like 2
semaphorin-J

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001281880.2NP_001268809.1  semaphorin-4D isoform 1 precursor

    See identical proteins and their annotated locations for NP_001268809.1

    Status: VALIDATED

    Source sequence(s)
    AC126247, AC126547
    Consensus CDS
    CCDS26514.1
    UniProtKB/Swiss-Prot
    O09126, Q6GTM9
    UniProtKB/TrEMBL
    Q8BJC1
    Related
    ENSMUSP00000105667.3, ENSMUST00000110040.9
    Conserved Domains (4) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
    cd00096
    Location:569577
    Ig; Ig strand B [structural motif]
    cl11960
    Location:563646
    Ig; Immunoglobulin domain
  2. NM_001378313.1NP_001365242.1  semaphorin-4D isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126547
    UniProtKB/Swiss-Prot
    O09126, Q6GTM9
    UniProtKB/TrEMBL
    Q8BJC1
    Conserved Domains (4) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
    cd00096
    Location:569577
    Ig; Ig strand B [structural motif]
    cl11960
    Location:563646
    Ig; Immunoglobulin domain
  3. NM_001378314.1NP_001365243.1  semaphorin-4D isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126547
    UniProtKB/Swiss-Prot
    O09126, Q6GTM9
    UniProtKB/TrEMBL
    Q8BJC1
    Conserved Domains (4) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
    cd00096
    Location:569577
    Ig; Ig strand B [structural motif]
    cl11960
    Location:563646
    Ig; Immunoglobulin domain
  4. NM_001378315.1NP_001365244.1  semaphorin-4D isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126547
    UniProtKB/Swiss-Prot
    O09126, Q6GTM9
    UniProtKB/TrEMBL
    Q8BJC1
    Conserved Domains (4) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
    cd00096
    Location:569577
    Ig; Ig strand B [structural motif]
    cl11960
    Location:563646
    Ig; Immunoglobulin domain
  5. NM_001378316.1NP_001365245.1  semaphorin-4D isoform 1 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126547
    UniProtKB/Swiss-Prot
    O09126, Q6GTM9
    UniProtKB/TrEMBL
    Q8BJC1
    Related
    ENSMUSP00000105666.2, ENSMUST00000110039.2
    Conserved Domains (4) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
    cd00096
    Location:569577
    Ig; Ig strand B [structural motif]
    cl11960
    Location:563646
    Ig; Immunoglobulin domain
  6. NM_001378317.1NP_001365246.1  semaphorin-4D isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126247, AC126547
    Conserved Domains (4) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
    cd00096
    Location:569577
    Ig; Ig strand B [structural motif]
    cl11960
    Location:563646
    Ig; Immunoglobulin domain
  7. NM_001378318.1NP_001365247.1  semaphorin-4D isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126547
    Conserved Domains (4) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
    cd00096
    Location:569577
    Ig; Ig strand B [structural motif]
    cl11960
    Location:563646
    Ig; Immunoglobulin domain
  8. NM_001378319.1NP_001365248.1  semaphorin-4D isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126547
    Conserved Domains (4) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
    cd00096
    Location:569577
    Ig; Ig strand B [structural motif]
    cl11960
    Location:563646
    Ig; Immunoglobulin domain
  9. NM_001378320.1NP_001365249.1  semaphorin-4D isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126247, AC126547
    Conserved Domains (2) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
  10. NM_001378321.1NP_001365250.1  semaphorin-4D isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126247, AC126547
    Conserved Domains (2) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
  11. NM_001378322.1NP_001365251.1  semaphorin-4D isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126547
    Conserved Domains (2) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
  12. NM_001378323.1NP_001365252.1  semaphorin-4D isoform 3 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126547
    Conserved Domains (2) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
  13. NM_001378324.1NP_001365253.1  semaphorin-4D isoform 4 precursor

    Status: VALIDATED

    Source sequence(s)
    AC126247, AC126547
    Conserved Domains (2) summary
    cd11259
    Location:31499
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:501546
    PSI; Plexin repeat
  14. NM_001378325.1NP_001365254.1  semaphorin-4D isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC126547
    UniProtKB/TrEMBL
    D3Z3P4
    Related
    ENSMUSP00000105669.3, ENSMUST00000110042.3
    Conserved Domains (2) summary
    cd00096
    Location:6371
    Ig; Ig strand B [structural motif]
    cl11960
    Location:55139
    Ig; Immunoglobulin domain
  15. NM_013660.5NP_038688.2  semaphorin-4D isoform 1 precursor

    See identical proteins and their annotated locations for NP_038688.2

    Status: VALIDATED

    Source sequence(s)
    AC126247, AC126547
    Consensus CDS
    CCDS26514.1
    UniProtKB/Swiss-Prot
    O09126, Q6GTM9
    UniProtKB/TrEMBL
    Q8BJC1
    Related
    ENSMUSP00000021900.8, ENSMUST00000021900.14
    Conserved Domains (4) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
    cd00096
    Location:569577
    Ig; Ig strand B [structural motif]
    cl11960
    Location:563646
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000079.7 Reference GRCm39 C57BL/6J

    Range
    51839565..51947823 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036157947.1XP_036013840.1  semaphorin-4D isoform X3

    Conserved Domains (2) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
  2. XM_036157945.1XP_036013838.1  semaphorin-4D isoform X1

    Conserved Domains (4) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
    cd00096
    Location:569577
    Ig; Ig strand B [structural motif]
    cl11960
    Location:563646
    Ig; Immunoglobulin domain
  3. XM_036157946.1XP_036013839.1  semaphorin-4D isoform X2

    Conserved Domains (2) summary
    cd11259
    Location:31501
    Sema_4D; The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100)
    pfam01437
    Location:503548
    PSI; Plexin repeat
  4. XM_036157948.1XP_036013841.1  semaphorin-4D isoform X4

    UniProtKB/TrEMBL
    D3Z3P4
    Conserved Domains (2) summary
    cd00096
    Location:6371
    Ig; Ig strand B [structural motif]
    cl11960
    Location:55139
    Ig; Immunoglobulin domain

RNA

  1. XR_004938006.1 RNA Sequence

  2. XR_004938005.1 RNA Sequence

  3. XR_004938004.1 RNA Sequence

  4. XR_004937990.1 RNA Sequence

  5. XR_004937993.1 RNA Sequence

  6. XR_004937991.1 RNA Sequence

  7. XR_004937992.1 RNA Sequence

  8. XR_004937995.1 RNA Sequence

  9. XR_004937994.1 RNA Sequence

  10. XR_004938007.1 RNA Sequence

  11. XR_004938003.1 RNA Sequence

  12. XR_004938000.1 RNA Sequence

  13. XR_004937986.1 RNA Sequence

  14. XR_004937988.1 RNA Sequence

  15. XR_004937987.1 RNA Sequence

  16. XR_004937989.1 RNA Sequence

  17. XR_004938001.1 RNA Sequence

  18. XR_004937999.1 RNA Sequence

  19. XR_004937996.1 RNA Sequence

  20. XR_004938002.1 RNA Sequence

  21. XR_004937997.1 RNA Sequence

  22. XR_004937998.1 RNA Sequence