Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

SLC6A4 (solute carrier family 6 member 4)

Identity

Other names5-HTT
5-HTTLPR
5HTT
HTT
OCD1
SERT
SERT1
hSERT
HGNC (Hugo) SLC6A4
LocusID (NCBI) 6532
Atlas_Id 49951
Location 17q11.2  [Link to chromosome band 17q11]
Location_base_pair Starts at 28521337 and ends at 28562986 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
PIP4K2B (17q12) / SLC6A4 (17q11.2)PIP4K2B 17q12 / SLC6A4 17q11.2

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)SLC6A4   11050
Cards
Entrez_Gene (NCBI)SLC6A4  6532  solute carrier family 6 member 4
Aliases5-HTT; 5-HTTLPR; 5HTT; HTT; 
OCD1; SERT; SERT1; hSERT
GeneCards (Weizmann)SLC6A4
Ensembl hg19 (Hinxton)ENSG00000108576 [Gene_View]  chr17:28521337-28562986 [Contig_View]  SLC6A4 [Vega]
Ensembl hg38 (Hinxton)ENSG00000108576 [Gene_View]  chr17:28521337-28562986 [Contig_View]  SLC6A4 [Vega]
ICGC DataPortalENSG00000108576
TCGA cBioPortalSLC6A4
AceView (NCBI)SLC6A4
Genatlas (Paris)SLC6A4
WikiGenes6532
SOURCE (Princeton)SLC6A4
Genomic and cartography
GoldenPath hg19 (UCSC)SLC6A4  -     chr17:28521337-28562986 -  17q11.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SLC6A4  -     17q11.2   [Description]    (hg38-Dec_2013)
EnsemblSLC6A4 - 17q11.2 [CytoView hg19]  SLC6A4 - 17q11.2 [CytoView hg38]
Mapping of homologs : NCBISLC6A4 [Mapview hg19]  SLC6A4 [Mapview hg38]
OMIM164230   182138   607834   
Gene and transcription
Genbank (Entrez)AA700070 AK308014 AK309538 AK313166 AU138385
RefSeq transcript (Entrez)NM_001045
RefSeq genomic (Entrez)NC_000017 NC_018928 NG_011747 NT_010783 NW_004929407
Consensus coding sequences : CCDS (NCBI)SLC6A4
Cluster EST : UnigeneHs.134662 [ NCBI ]
CGAP (NCI)Hs.134662
Alternative Splicing GalleryENSG00000108576
Gene ExpressionSLC6A4 [ NCBI-GEO ]   SLC6A4 [ EBI - ARRAY_EXPRESS ]   SLC6A4 [ SEEK ]   SLC6A4 [ MEM ]
Gene Expression Viewer (FireBrowse)SLC6A4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6532
GTEX Portal (Tissue expression)SLC6A4
Protein : pattern, domain, 3D structure
UniProt/SwissProtP31645 (Uniprot)
NextProtP31645  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP31645
Splice isoforms : SwissVarP31645 (Swissvar)
PhosPhoSitePlusP31645
Domaine pattern : Prosite (Expaxy)NA_NEUROTRAN_SYMP_1 (PS00610)    NA_NEUROTRAN_SYMP_2 (PS00754)    NA_NEUROTRAN_SYMP_3 (PS50267)   
Domains : Interpro (EBI)Na/ntran_symport    Na/ntran_symport_serotonin_N   
Domain families : Pfam (Sanger)5HT_transport_N (PF03491)    SNF (PF00209)   
Domain families : Pfam (NCBI)pfam03491    pfam00209   
DMDM Disease mutations6532
Blocks (Seattle)SLC6A4
SuperfamilyP31645
Human Protein AtlasENSG00000108576
Peptide AtlasP31645
HPRD01640
IPIIPI00790986   IPI00797748   
Protein Interaction databases
DIP (DOE-UCLA)P31645
IntAct (EBI)P31645
FunCoupENSG00000108576
BioGRIDSLC6A4
STRING (EMBL)SLC6A4
ZODIACSLC6A4
Ontologies - Pathways
QuickGOP31645
Ontology : AmiGOresponse to hypoxia  serotonin:sodium symporter activity  serotonin:sodium symporter activity  protein binding  cytosol  plasma membrane  integral component of plasma membrane  integral component of plasma membrane  serotonin transport  synaptic transmission  response to nutrient  memory  circadian rhythm  monoamine transmembrane transporter activity  response to toxic substance  endosome membrane  positive regulation of gene expression  endomembrane system  serotonin transmembrane transporter activity  serotonin transmembrane transporter activity  monoamine transport  myosin binding  syntaxin-1 binding  Rab GTPase binding  cocaine binding  thalamus development  negative regulation of cerebellar granule cell precursor proliferation  negative regulation of synaptic transmission, dopaminergic  response to estradiol  social behavior  vasoconstriction  response to drug  sperm ejaculation  protein homodimerization activity  neuron projection  membrane raft  negative regulation of neuron differentiation  positive regulation of cell cycle  negative regulation of organ growth  metal ion binding  brain morphogenesis  nitric-oxide synthase binding  actin filament binding  protein oligomerization  protein homooligomerization  serotonin uptake  serotonin uptake  transmembrane transport  cellular response to retinoic acid  cellular response to cGMP  presynapse  presynapse  presynapse  
Ontology : EGO-EBIresponse to hypoxia  serotonin:sodium symporter activity  serotonin:sodium symporter activity  protein binding  cytosol  plasma membrane  integral component of plasma membrane  integral component of plasma membrane  serotonin transport  synaptic transmission  response to nutrient  memory  circadian rhythm  monoamine transmembrane transporter activity  response to toxic substance  endosome membrane  positive regulation of gene expression  endomembrane system  serotonin transmembrane transporter activity  serotonin transmembrane transporter activity  monoamine transport  myosin binding  syntaxin-1 binding  Rab GTPase binding  cocaine binding  thalamus development  negative regulation of cerebellar granule cell precursor proliferation  negative regulation of synaptic transmission, dopaminergic  response to estradiol  social behavior  vasoconstriction  response to drug  sperm ejaculation  protein homodimerization activity  neuron projection  membrane raft  negative regulation of neuron differentiation  positive regulation of cell cycle  negative regulation of organ growth  metal ion binding  brain morphogenesis  nitric-oxide synthase binding  actin filament binding  protein oligomerization  protein homooligomerization  serotonin uptake  serotonin uptake  transmembrane transport  cellular response to retinoic acid  cellular response to cGMP  presynapse  presynapse  presynapse  
Pathways : KEGGSerotonergic synapse   
NDEx Network
Atlas of Cancer Signalling NetworkSLC6A4
Wikipedia pathwaysSLC6A4
Orthology - Evolution
OrthoDB6532
GeneTree (enSembl)ENSG00000108576
Phylogenetic Trees/Animal Genes : TreeFamSLC6A4
Homologs : HomoloGeneSLC6A4
Homology/Alignments : Family Browser (UCSC)SLC6A4
Gene fusions - Rearrangements
Fusion: TCGAPIP4K2B 17q12 SLC6A4 17q11.2 BRCA
Polymorphisms : SNP, variants
NCBI Variation ViewerSLC6A4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SLC6A4
dbVarSLC6A4
ClinVarSLC6A4
1000_GenomesSLC6A4 
Exome Variant ServerSLC6A4
ExAC (Exome Aggregation Consortium)SLC6A4 (select the gene name)
Genetic variants : HAPMAP6532
Genomic Variants (DGV)SLC6A4 [DGVbeta]
Mutations
ICGC Data PortalSLC6A4 
TCGA Data PortalSLC6A4 
Broad Tumor PortalSLC6A4
OASIS PortalSLC6A4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSLC6A4 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SLC6A4
DgiDB (Drug Gene Interaction Database)SLC6A4
DoCM (Curated mutations)SLC6A4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SLC6A4 (select a term)
intoGenSLC6A4
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)17:28521337-28562986  ENSG00000108576
CONAN: Copy Number AnalysisSLC6A4 
Mutations and Diseases : HGMDSLC6A4
OMIM164230    182138    607834   
MedgenSLC6A4
Genetic Testing Registry SLC6A4
NextProtP31645 [Medical]
TSGene6532
GENETestsSLC6A4
Huge Navigator SLC6A4 [HugePedia]
snp3D : Map Gene to Disease6532
BioCentury BCIQSLC6A4
ClinGenSLC6A4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6532
Chemical/Pharm GKB GenePA312
Clinical trialSLC6A4
Miscellaneous
canSAR (ICR)SLC6A4 (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSLC6A4
EVEXSLC6A4
GoPubMedSLC6A4
iHOPSLC6A4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Aug 9 19:09:23 CEST 2016

Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.