Gene: SLC6A4

Basic information

Tag Content
Uniprot ID P31645; Q5EE02;
Entrez ID 6532
Genbank protein ID ABV02581.1; AAH69484.1; CAA50029.1; AAB93475.1; AAA35492.1; AAW80933.1;
Genbank nucleotide ID NM_001045.5
Ensembl protein ID ENSP00000261707; ENSP00000385822; ENSP00000498537;
Ensembl nucleotide ID ENSG00000108576
Gene name Sodium-dependent serotonin transporter
Gene symbol SLC6A4
Organism Homo sapiens
NCBI taxa ID 9606
Cleft type
Developmental stage
Data sources Manually collected
Reference 22072571
Functional description Serotonin transporter whose primary function in the central nervous system involves the regulation of serotonergic signaling via transport of serotonin molecules from the synaptic cleft back into the pre-synaptic terminal for re-utilization. Plays a key role in mediating regulation of the availability of serotonin to other receptors of serotonergic systems. Terminates the action of serotonin and recycles it in a sodium-dependent manner.
Sequence
METTPLNSQK QLSACEDGED CQENGVLQKV VPTPGDKVES GQISNGYSAV PSPGAGDDTR 60
HSIPATTTTL VAELHQGERE TWGKKVDFLL SVIGYAVDLG NVWRFPYICY QNGGGAFLLP 120
YTIMAIFGGI PLFYMELALG QYHRNGCISI WRKICPIFKG IGYAICIIAF YIASYYNTIM 180
AWALYYLISS FTDQLPWTSC KNSWNTGNCT NYFSEDNITW TLHSTSPAEE FYTRHVLQIH 240
RSKGLQDLGG ISWQLALCIM LIFTVIYFSI WKGVKTSGKV VWVTATFPYI ILSVLLVRGA 300
TLPGAWRGVL FYLKPNWQKL LETGVWIDAA AQIFFSLGPG FGVLLAFASY NKFNNNCYQD 360
ALVTSVVNCM TSFVSGFVIF TVLGYMAEMR NEDVSEVAKD AGPSLLFITY AEAIANMPAS 420
TFFAIIFFLM LITLGLDSTF AGLEGVITAV LDEFPHVWAK RRERFVLAVV ITCFFGSLVT 480
LTFGGAYVVK LLEEYATGPA VLTVALIEAV AVSWFYGITQ FCRDVKEMLG FSPGWFWRIC 540
WVAISPLFLL FIICSFLMSP PQLRLFQYNY PYWSIILGYC IGTSSFICIP TYIAYRLIIT 600
PGTFKERIIK SITPETPTEI PCGDIRLNAV

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression information

Gene expression in different tissues (GTEx V7)

  

Gene expression in different tissues (ENCODE)

  

Protein structural annotations

3D structure in PDB database

Protein disorder information

Orthologous information

Relation Gene symbol Entrez ID UniProt ID Cleft type Developmental stage Species Evidence Details
1:1 orthologSLC6A4491184F1PXA1Canis lupus familiarisPredictionMore>>
1:1 orthologSLC6A4102172383A0A452DQ43Capra hircusPredictionMore>>
1:1 orthologSLC6A4100033848F6QG30Equus caballusPredictionMore>>
1:1 orthologSLC6A46532P31645Homo sapiensPublicationMore>>
1:1 orthologSlc6a415567Q60857Mus musculusPredictionMore>>
1:1 orthologSLC6A4468201A0A2J8LIN5Pan troglodytesPredictionMore>>
1:1 orthologSLC6A4G1SK44Oryctolagus cuniculusPredictionMore>>
1:1 orthologSlc6a425553P31652Rattus norvegicusPredictionMore>>
1:1 orthologslc6a4a664719Q1WGB5Danio rerioPredictionMore>>

Identified variants/mutations related to cleft phenotype

Gene symbol Significant Variants/SNPS Methods PubMed ID
SLC6A4rs1042173PCR-RFLP22072571
SLC6A4rs4583306PCR-RFLP22072571
SLC6A4rs2020942PCR-RFLP22072571

Other genetic variants/mutations

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Disease or phenotype associated information

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Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID GO Term Evidence
GO:0005335 serotonin:sodium symporter activityIBA
GO:0005335 serotonin:sodium symporter activityIDA
GO:0005335 serotonin:sodium symporter activityTAS
GO:0005515 protein bindingIPI
GO:0008504 monoamine transmembrane transporter activityIDA
GO:0017075 syntaxin-1 bindingIEA
GO:0019811 cocaine bindingIEA
GO:0042802 identical protein bindingISS
GO:0046872 metal ion bindingIEA
GO:0050998 nitric-oxide synthase bindingIEA
GO:0051015 actin filament bindingISS
GO:0051378 serotonin bindingIBA

GO:Biological Process

GO ID GO Term Evidence
GO:0001666 response to hypoxiaIEA
GO:0007584 response to nutrientIEA
GO:0007613 memoryIEA
GO:0007623 circadian rhythmIEA
GO:0009636 response to toxic substanceIDA
GO:0010628 positive regulation of gene expressionIEA
GO:0014064 positive regulation of serotonin secretionIEA
GO:0015844 monoamine transportIDA
GO:0021941 negative regulation of cerebellar granule cell precursor proliferationIEA
GO:0032227 negative regulation of synaptic transmission, dopaminergicIEA
GO:0032355 response to estradiolIEA
GO:0035176 social behaviorISS
GO:0042136 neurotransmitter biosynthetic processTAS
GO:0042310 vasoconstrictionIEA
GO:0042493 response to drugIEA
GO:0042713 sperm ejaculationIEA
GO:0045665 negative regulation of neuron differentiationIEA
GO:0045787 positive regulation of cell cycleIEA
GO:0046621 negative regulation of organ growthISS
GO:0048854 brain morphogenesisISS
GO:0051610 serotonin uptakeIDA
GO:0051610 serotonin uptakeIBA
GO:0051610 serotonin uptakeIMP
GO:0055085 transmembrane transportIEA
GO:0071300 cellular response to retinoic acidIEA
GO:0071321 cellular response to cGMPIEA
GO:0090067 regulation of thalamus sizeIMP

GO:Cellular Component

GO ID GO Term Evidence
GO:0005886 plasma membraneIDA
GO:0005886 plasma membraneIBA
GO:0005886 plasma membraneTAS
GO:0005925 focal adhesionISS
GO:0010008 endosome membraneIEA
GO:0012505 endomembrane systemIDA
GO:0043005 neuron projectionIBA
GO:0045121 membrane raftIDA
GO:0045202 synapseISS
GO:0099055 integral component of postsynaptic membraneIEA
GO:0099056 integral component of presynaptic membraneIEA
GO:0099154 serotonergic synapseIEA

Reactome Pathway

Reactome ID Reactome Term Evidence
R-HSA-112311 Neurotransmitter clearanceTAS
R-HSA-112315 Transmission across Chemical SynapsesTAS
R-HSA-112316 Neuronal SystemTAS
R-HSA-380615 Serotonin clearance from the synaptic cleftTAS

Drugs and compounds information

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Functional annotations

Keywords

Keyword ID Keyword Term
KW-0002 3D-structure
KW-0025 Alternative splicing
KW-0965 Cell junction
KW-1003 Cell membrane
KW-1015 Disulfide bond
KW-0967 Endosome
KW-0325 Glycoprotein
KW-0472 Membrane
KW-0479 Metal-binding
KW-0532 Neurotransmitter transport
KW-0597 Phosphoprotein
KW-0621 Polymorphism
KW-1185 Reference proteome
KW-0915 Sodium
KW-0769 Symport
KW-0770 Synapse
KW-0812 Transmembrane
KW-1133 Transmembrane helix
KW-0813 Transport

Interpro

InterPro ID InterPro Term
IPR000175 Na/ntran_symport
IPR013086 Na/ntran_symport_serotonin_N
IPR037272 SNS_sf

PROSITE

PROSITE ID PROSITE Term
PS00610 NA_NEUROTRAN_SYMP_1
PS00754 NA_NEUROTRAN_SYMP_2
PS50267 NA_NEUROTRAN_SYMP_3

Pfam

Pfam ID Pfam Term
PF03491 5HT_transport_N
PF00209 SNF

Protein-protein interaction

Protein-miRNA interaction