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SEMA6D semaphorin 6D [ Homo sapiens (human) ]

Gene ID: 80031, updated on 14-Nov-2024

Summary

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Official Symbol
SEMA6Dprovided by HGNC
Official Full Name
semaphorin 6Dprovided by HGNC
Primary source
HGNC:HGNC:16770
See related
Ensembl:ENSG00000137872 MIM:609295; AllianceGenome:HGNC:16770
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
Summary
Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]
Expression
Broad expression in small intestine (RPKM 13.9), placenta (RPKM 10.4) and 19 other tissues See more
Orthologs
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Genomic context

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See SEMA6D in Genome Data Viewer
Location:
15q21.1
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (47184089..47774228)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (44992008..45582270)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (47476286..48066425)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene cytochrome b5 type B-like Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:47425847-47426471 Neighboring gene uncharacterized LOC107984733 Neighboring gene RN7SK pseudogene 139 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:47697799-47698547 Neighboring gene uncharacterized LOC124900620 Neighboring gene uncharacterized LOC105370804 Neighboring gene Sharpr-MPRA regulatory region 212 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:48056535-48057734 Neighboring gene ribosomal protein L7a pseudogene 62 Neighboring gene LINC01491 intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9371 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:48143210-48144409 Neighboring gene long intergenic non-protein coding RNA 1491 Neighboring gene uncharacterized LOC124900354 Neighboring gene uncharacterized LOC102724553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9372 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9374

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Expression of semaphorin 6D in gastric carcinoma and its significance. Zhao XY, et al. World J Gastroenterol, 2006 Dec 7. PMID 17143962, Free PMC Article
  2. Neuroimaging genetic associations between SEMA6D, brain structure, and reading skills. Thomas T, et al. J Clin Exp Neuropsychol, 2021 Apr. PMID 33960276, Free PMC Article
  3. Knowing how to navigate: mechanisms of semaphorin signaling in the nervous system. He Z, et al. Sci STKE, 2002 Feb 12. PMID 11842242
  4. Semaphorin 6D tunes amygdalar circuits for emotional, metabolic, and inflammatory outputs. Nakanishi Y, et al. Neuron, 2024 Sep 4. PMID 39002542
  5. [Semaphorin 6D and Snail are highly expressed in gastric cancer and positively correlated with malignant clinicopathological indexes]. Qu S, et al. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi, 2019 Oct. PMID 31814570

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Semaphorin 6D tunes amygdalar circuits for emotional, metabolic, and inflammatory outputs.
    Title: Semaphorin 6D tunes amygdalar circuits for emotional, metabolic, and inflammatory outputs.
  2. Neuroimaging genetic associations between SEMA6D, brain structure, and reading skills.
    Title: Neuroimaging genetic associations between SEMA6D, brain structure, and reading skills.
  3. CircUBAP2 promotes SEMA6D expression to enhance the cisplatin resistance in osteosarcoma through sponging miR-506-3p by activating Wnt/beta-catenin signaling pathway.
    Title: CircUBAP2 promotes SEMA6D expression to enhance the cisplatin resistance in osteosarcoma through sponging miR-506-3p by activating Wnt/β-catenin signaling pathway.
  4. The high expression of SEMA6D and Snail in gastric cancer are related to the malignant clinicopathological indexes of gastric cancer.
    Title: [Semaphorin 6D and Snail are highly expressed in gastric cancer and positively correlated with malignant clinicopathological indexes].
  5. Study provide the first evidence that SEMA3C, SEMA5A and SEMA6D can be considered as markers of liver injury in chronic hepatitis C. While serum concentrations of SEMA3C and SEMA6D significantly increased with fibrosis stage in both HCV-g1 and HCV-g3 infections, the concentration of SEMA5A inversely correlated with fibrosis stage in both HCV genotypes.
    Title: The association of semaphorins 3C, 5A and 6D with liver fibrosis stage in chronic hepatitis C.
  6. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  8. Semaphorin 6D may play an important role in the occurrence and development of gastric carcinoma, and is related to tumor angiogenesis.
    Title: Expression of semaphorin 6D in gastric carcinoma and its significance.
  9. identification, characterization, and functional study of the two novel human members of the semaphorin gene family
    Title: Identification, characterization, and functional study of the two novel human members of the semaphorin gene family.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome wide association study (GWAS) providing evidence of an association between common genetic variants and late radiotherapy toxicity.
EBI GWAS Catalog
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.
EBI GWAS Catalog
Genetics of coronary artery calcification among African Americans, a meta-analysis.
EBI GWAS Catalog
Genome-wide association analysis of eating disorder-related symptoms, behaviors, and personality traits.
EBI GWAS Catalog
Novel genetic variants modify the effect of smoking on carotid plaque burden in Hispanics.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ11598, KIAA1479

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chemorepellent activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables receptor ligand activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of axon extension IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of smooth muscle cell migration IEA
Inferred from Electronic Annotation
more info
  
involved_in neural crest cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of smooth muscle cell migration IEA
Inferred from Electronic Annotation
more info
  
involved_in semaphorin-plexin signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in semaphorin-plexin signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in smooth muscle cell migration IEA
Inferred from Electronic Annotation
more info
  
involved_in ventricular system development IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
located_in cell surface IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in cytoplasm IMP
Inferred from Mutant Phenotype
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
semaphorin-6D
Names
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D

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_029119.2 RefSeqGene

    Range
    538300..595023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001198999.2 → NP_001185928.1  semaphorin-6D isoform 1 precursor

    See identical proteins and their annotated locations for NP_001185928.1

    Status: REVIEWED

    Source sequence(s)
    AC066615, AF389427, BC150253
    Consensus CDS
    CCDS32224.1
    UniProtKB/TrEMBL
    A0A185QE25
    Related
    ENSP00000452815.1, ENST00000558014.5
    Conserved Domains (3) summary
    cd11269
    Location:49 → 513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514 → 543
    PSI; Plexin repeat
    cl25496
    Location:869 → 1005
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

  2. NM_001358351.3 → NP_001345280.1  semaphorin-6D isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AC018900, AF389426, AK290032
    Consensus CDS
    CCDS32225.1
    UniProtKB/Swiss-Prot
    A6NF10, A6NM95, A6NNK1, A7E2A0, Q8NFY3, Q8NFY4, Q8NFY5, Q8NFY6, Q8NFY7, Q9P249
    UniProtKB/TrEMBL
    A8K1W7
    Related
    ENSP00000446152.3, ENST00000536845.7
    Conserved Domains (3) summary
    cd11269
    Location:49 → 513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514 → 569
    PSI; Plexin repeat
    cl25496
    Location:931 → 1067
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

  3. NM_001358352.2 → NP_001345281.1  semaphorin-6D isoform 7 precursor

    Status: REVIEWED

    Source sequence(s)
    AC018900, AC044787, AF389428
    UniProtKB/TrEMBL
    A8K1W7
    Conserved Domains (3) summary
    cd11269
    Location:49 → 513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514 → 543
    PSI; Plexin repeat
    cl25496
    Location:944 → 1080
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

  4. NM_020858.2 → NP_065909.1  semaphorin-6D isoform 1 precursor

    See identical proteins and their annotated locations for NP_065909.1

    Status: REVIEWED

    Source sequence(s)
    AC044787, AF389430
    Consensus CDS
    CCDS32224.1
    UniProtKB/TrEMBL
    A0A185QE25
    Related
    ENSP00000350770.4, ENST00000358066.8
    Conserved Domains (3) summary
    cd11269
    Location:49 → 513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514 → 543
    PSI; Plexin repeat
    cl25496
    Location:869 → 1005
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

  5. NM_024966.3 → NP_079242.2  semaphorin-6D isoform 6 precursor

    See identical proteins and their annotated locations for NP_079242.2

    Status: REVIEWED

    Source sequence(s)
    AC018900, AC044787, AF389426
    Consensus CDS
    CCDS32229.1
    UniProtKB/Swiss-Prot
    Q8NFY4
    Related
    ENSP00000374076.3, ENST00000389425.7
    Conserved Domains (1) summary
    cl15693
    Location:49 → 476
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins

  6. NM_153616.2 → NP_705869.1  semaphorin-6D isoform 2 precursor

    See identical proteins and their annotated locations for NP_705869.1

    Status: REVIEWED

    Source sequence(s)
    AC044787, AF389427
    Consensus CDS
    CCDS32227.1
    UniProtKB/TrEMBL
    A0A185QE25
    Related
    ENSP00000374079.3, ENST00000389428.7
    Conserved Domains (2) summary
    cd11269
    Location:49 → 513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514 → 569
    PSI; Plexin repeat

  7. NM_153617.2 → NP_705870.1  semaphorin-6D isoform 3 precursor

    See identical proteins and their annotated locations for NP_705870.1

    Status: REVIEWED

    Source sequence(s)
    AC044787, AF389428
    Consensus CDS
    CCDS32226.1
    UniProtKB/TrEMBL
    A8K1W7
    Related
    ENSP00000346786.4, ENST00000354744.8
    Conserved Domains (2) summary
    cd11269
    Location:49 → 513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514 → 569
    PSI; Plexin repeat

  8. NM_153618.2 → NP_705871.1  semaphorin-6D isoform 4 precursor

    See identical proteins and their annotated locations for NP_705871.1

    Status: REVIEWED

    Source sequence(s)
    AC044787, AF389429
    Consensus CDS
    CCDS32225.1
    UniProtKB/Swiss-Prot
    A6NF10, A6NM95, A6NNK1, A7E2A0, Q8NFY3, Q8NFY4, Q8NFY5, Q8NFY6, Q8NFY7, Q9P249
    UniProtKB/TrEMBL
    A8K1W7
    Related
    ENSP00000324857.5, ENST00000316364.9
    Conserved Domains (3) summary
    cd11269
    Location:49 → 513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514 → 569
    PSI; Plexin repeat
    cl25496
    Location:931 → 1067
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

  9. NM_153619.1 → NP_705872.1  semaphorin-6D isoform 5 precursor

    See identical proteins and their annotated locations for NP_705872.1

    Status: REVIEWED

    Source sequence(s)
    AF389427, BC004330
    Consensus CDS
    CCDS32228.1
    UniProtKB/Swiss-Prot
    Q8NFY4
    Related
    ENSP00000348276.3, ENST00000355997.7
    Conserved Domains (2) summary
    cd11269
    Location:49 → 513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514 → 569
    PSI; Plexin repeat

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    47184089..47774228
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    44992008..45582270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NFY4.1 GenPept UniProtKB/Swiss-Prot:Q8NFY4

Gene LinkOut

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