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SEMA6D semaphorin 6D [ Homo sapiens (human) ]

Gene ID: 80031, updated on 7-Sep-2023

Summary

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

See SEMA6D in Genome Data Viewer
Location:
15q21.1
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (47184089..47774228)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (44992008..45582270)
105.20220307 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 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

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

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
PubMed 
enables semaphorin receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in axon guidance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of axon extension involved in axon guidance IBA
Inferred from Biological aspect of Ancestor
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
PubMed 
involved_in positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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_001198999.2NP_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/Swiss-Prot
    Q8NFY4
    UniProtKB/TrEMBL
    A0A185QE25
    Related
    ENSP00000452815.1, ENST00000558014.5
    Conserved Domains (3) summary
    cd11269
    Location:49513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514543
    PSI; Plexin repeat
    cl25496
    Location:8691005
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  2. NM_001358351.3NP_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:49513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl25496
    Location:9311067
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  3. NM_001358352.2NP_001345281.1  semaphorin-6D isoform 7 precursor

    Status: REVIEWED

    Source sequence(s)
    AC018900, AC044787, AF389428
    UniProtKB/TrEMBL
    A8K1W7
    Conserved Domains (3) summary
    cd11269
    Location:49513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514543
    PSI; Plexin repeat
    cl25496
    Location:9441080
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  4. NM_020858.2NP_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/Swiss-Prot
    Q8NFY4
    UniProtKB/TrEMBL
    A0A185QE25
    Related
    ENSP00000350770.4, ENST00000358066.8
    Conserved Domains (3) summary
    cd11269
    Location:49513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514543
    PSI; Plexin repeat
    cl25496
    Location:8691005
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  5. NM_024966.3NP_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:49476
    Sema; The Sema domain, a protein interacting module, of semaphorins and plexins
  6. NM_153616.2NP_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/Swiss-Prot
    Q8NFY4
    UniProtKB/TrEMBL
    A0A185QE25
    Related
    ENSP00000374079.3, ENST00000389428.7
    Conserved Domains (2) summary
    cd11269
    Location:49513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514569
    PSI; Plexin repeat
  7. NM_153617.2NP_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/Swiss-Prot
    Q8NFY4
    UniProtKB/TrEMBL
    A8K1W7
    Related
    ENSP00000346786.4, ENST00000354744.8
    Conserved Domains (2) summary
    cd11269
    Location:49513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514569
    PSI; Plexin repeat
  8. NM_153618.2NP_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:49513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514569
    PSI; Plexin repeat
    cl25496
    Location:9311067
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
  9. NM_153619.1NP_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:49513
    Sema_6D; The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D)
    pfam01437
    Location:514569
    PSI; Plexin repeat

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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)