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    SEMA6D semaphorin 6D [ Homo sapiens (human) ]

    Gene ID: 80031, updated on 29-Oct-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
    mouse all
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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 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)

    Genotypes

    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 neuropilin binding 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 chemotaxis 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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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