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SLC6A16 Gene

protein-coding   GIFtS: 49
GCID: GC19M049792

Solute Carrier Family 6, Member 16

(Previous names: solute carrier family 6 (neurotransmitter transporter),...)
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Solute Carrier Family 6, Member 161 2     NTT5 Protein1
Solute Carrier Family 6 (Neurotransmitter Transporter), Member 161 2     Orphan Sodium- And Chloride-Dependent Neurotransmitter Transporter NTT52
NTT52 3     Solute Carrier Family 6 Member 163
NT52 5     

External Ids:    HGNC: 136221   Entrez Gene: 289682   Ensembl: ENSG000000631277   OMIM: 6079725   UniProtKB: Q9GZN63   

Export aliases for SLC6A16 gene to outside databases

Previous GC identifers: GC00U990833 GC19M054484 GC19M046169


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SLC6A16 Gene:
SLC6A16 shows structural characteristics of an Na(+)- and Cl(-)-dependent neurotransmitter transporter, including
12 transmembrane (TM) domains, intracellular N and C termini, and large extracellular loops containing multiple
N-glycosylation sites.(supplied by OMIM, Mar 2008)

GeneCards Summary for SLC6A16 Gene:
SLC6A16 (solute carrier family 6, member 16) is a protein-coding gene. Diseases associated with SLC6A16 include prostatitis. GO annotations related to this gene include neurotransmitter:sodium symporter activity and neurotransmitter transporter activity. An important paralog of this gene is SLC6A15.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000019.10  NT_011109.17  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SLC6A16 gene promoter:
         RP58   USF1   GCNF   Lmo2   USF2   USF-1:USF-2   HEN1   USF-1   HFH-1   Zic3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSLC6A16 promoter sequence
   Search Chromatin IP Primers for SLC6A16

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLC6A16


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.33   Ensembl cytogenetic band:  19q13.33   HGNC cytogenetic band: 19q13.33

SLC6A16 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC6A16 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M049792:  view genomic region     (about GC identifiers)

Start:
49,792,889 bp from pter      End:
49,828,482 bp from pter
Size:
35,594 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: S6A16_HUMAN, Q9GZN6 (See protein sequence)
Recommended Name: Orphan sodium- and chloride-dependent neurotransmitter transporter NTT5  
Size: 736 amino acids; 82200 Da
Secondary accessions: Q9Y5I9

Explore the universe of human proteins at neXtProt for SLC6A16: NX_Q9GZN6

Explore proteomics data for SLC6A16 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn229

  • See SLC6A16 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_054756.2  
    ENSEMBL proteins: 
     ENSP00000338627   ENSP00000404022   ENSP00000469885   ENSP00000470623   ENSP00000472752  
     ENSP00000472191  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    SLC: Solute carriers

    IUPHAR Guide to PHARMACOLOGY protein family classification: NTT5
    Neutral amino acid transporter subfamily

    1 InterPro protein domain:
     IPR000175 Na/ntran_symport

    Graphical View of Domain Structure for InterPro Entry Q9GZN6

    ProtoNet protein and cluster: Q9GZN6

    UniProtKB/Swiss-Prot: S6A16_HUMAN, Q9GZN6
    Similarity: Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A16 subfamily


    SLC6A16 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005326neurotransmitter transporter activity NAS11112352
    GO:0005328neurotransmitter:sodium symporter activity IEA--
         
    SLC6A16 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SLC6A16:
     Increased gamma-H2AX phosphory 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SLC6A16
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    miRNA
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    miRTarBase miRNAs that target SLC6A16:
    hsa-mir-335-5p (MIRT018187), hsa-mir-34a-5p (MIRT025508), hsa-mir-26b-5p (MIRT029566)

    Block miRNA regulation of human, mouse, rat SLC6A16 using miScript Target Protectors
    2 qRT-PCR Assays for microRNAs that regulate SLC6A16:
    hsa-miR-29a* hsa-miR-4267
    SwitchGear 3'UTR luciferase reporter plasmidSLC6A16 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC6A16


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    S6A16_HUMAN, Q9GZN6: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    golgi apparatus1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular NAS11112352
    GO:0016021integral component of membrane IEA--

    SLC6A16 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SLC6A16
    Interactions:

        Search GeneGlobe Interaction Network for SLC6A16

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for SLC6A16 (ENSP000003386274) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    STX1AENSP000002228124STRING: ENSP00000222812
    TBL3ENSP000003318154STRING: ENSP00000331815
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006836neurotransmitter transport NAS11112352

    SLC6A16 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SLC6A16 (S6A16)

    1 HMDB Compound for SLC6A16    About this table
    CompoundSynonyms CAS #PubMed Ids
    SodiumSodium (see all 2)7440-23-5--



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SLC6A16 gene: 
    NM_014037.2  

    Unigene Cluster for SLC6A16:

    Solute carrier family 6, member 16
    Hs.130949  [show with all ESTs]
    Unigene Representative Sequence: BC034948
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000335875(uc002pmz.3) ENST00000454748(uc002pna.3) ENST00000598828
    ENST00000598221 ENST00000594180 ENST00000597969 ENST00000594917
    miRNA
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    2 qRT-PCR Assays for microRNAs that regulate SLC6A16:
    hsa-miR-29a* hsa-miR-4267
    SwitchGear 3'UTR luciferase reporter plasmidSLC6A16 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat SLC6A16

    Additional mRNA sequence: 

    AF151977.1 AF265578.1 AL136856.1 BC034948.1 BC039336.1 

    7 DOTS entries:

    DT.211403  DT.211404  DT.100748604  DT.95178079  DT.91746353  DT.91819915  DT.99989723 

    Selected AceView cDNA sequences (see all 60):

    AA609875 BI828550 BI826017 CD359331 CD300308 AA868681 AI208927 AL136856 
    AF265578 BX114792 BI828810 AI001939 BU617940 BI830620 BC039336 AA621413 
    BX112834 BC034948 AW665979 BG717391 AI478962 BI560607 AF151977 AA403002 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for SLC6A16    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b
    SP1:                                            -                       -                     
    SP2:                                            -                       -                     
    SP3:                                                                                          
    SP4:                                -     -                                                   


    ECgene alternative splicing isoforms for SLC6A16

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SLC6A16 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGCTGAGCA
    SLC6A16 Expression
    About this image


    SLC6A16 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 4) fully expand
     
     Testis (Reproductive System)    fully expand to see all 3 entries
             Leydig Cells Testis Interstitium
             Testis Interstitium
     
     Neural Ectoderm (Nervous System)
             Neural ectoderm cells
     
     Blood (Hematopoietic System)
             Mature B-Cells Peripheral Blood
     
     Neural Tube (Nervous System)
             Floor plate-like cells
    SLC6A16 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SLC6A16 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.130949

    UniProtKB/Swiss-Prot: S6A16_HUMAN, Q9GZN6
    Tissue specificity: Highly expressed in peripheral tissues, particularly in testis, pancreas, and prostate

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for SLC6A16 gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Slc6a161 , 5 solute carrier family 6, member 161, 5 67.09(n)1
    50.42(a)1
      7 (29.22 cM)5
    3818841  XM_355900.71  XP_355900.61 
     452410855 
    lizard
    (Anolis carolinensis)
    Reptilia SLC6A166
    solute carrier family 6, member 16
    36(a)
    1 ↔ 1
    GL343355.1(26562-34501)
    zebrafish
    (Danio rerio)
    Actinopterygii SLC6A16 (2 of 2)6
    SLC6A16 (1 of 2)6
    solute carrier family 6, member 16
    34(a)
    33(a)
    1 ↔ many
    1 ↔ many
    24(40126163-40158383) ENSDARG00000037422
    3(16186342-16215766) ENSDARG00000007129
    fruit fly
    (Drosophila melanogaster)
    Insecta CG430666
    CG108046
    --
    27(a)
    25(a)
    many ↔ many
    many ↔ many
    2R(14402081-14413944)
    X(3370722-3376355)


    ENSEMBL Gene Tree for SLC6A16 (if available)
    TreeFam Gene Tree for SLC6A16 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SLC6A16 gene
    SLC6A152  SLC6A172  SLC6A202  SLC6A182  SLC6A192  
    12 SIMAP similar genes for SLC6A16 using alignment to 6 protein entries:     S6A16_HUMAN (see all proteins):
    SLC6A4    DKFZp761I0921    SLC6A17    SLC6A15    SLC6A20    5HTT
    SLC6A9    SLC6A18    SLC6A11    SLC6A19    SLC6A7    SLC6A2

    SLC6A16 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SLC6A16 (see all 684)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1450296021,2
    --49792722(+) ATCTCA/GTGATA 1 -- ds50010--------
    rs1394329521,2
    C--49792790(+) CCTCA-/TTTTTT 1 -- ds50010--------
    rs582921841,2
    C,F--49792820(+) AAGAAA/GTGCCT 1 -- ds50012Minor allele frequency- G:0.15CSA WA 120
    rs1910511911,2
    --49792830(+) TTTCAC/TCTCCC 1 -- ds50010--------
    rs1476302581,2
    C--49793021(+) CAGTCC/TTTGGA 1 -- ut310--------
    rs1827643251,2
    C--49793034(+) TCCAGC/TAGACT 1 -- ut310--------
    rs1858202451,2
    --49793487(+) TAGGGA/TTGTGG 2 T S mis10--------
    rs1423091541,2
    C--49793508(+) AGGCCC/TGTCTC 2 R G mis10--------
    rs344862251,2
    C,F,H--49793509(+) GGCCCG/ATCTCC 2 /D syn19Minor allele frequency- A:0.01NS NA WA EU 2241
    rs348175631,2
    C,F--49793620(+) GCCCAC/TGGTGG 2 P syn15Minor allele frequency- T:0.01NA WA EU 1519

    HapMap Linkage Disequilibrium report for SLC6A16 (49792889 - 49828482 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for SLC6A16:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2658176CNV Deletion23128226
    dgv52n68CNV Loss17160897
    nsv912261CNV Loss21882294
    nsv9739CNV Gain+Loss18304495

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SLC6A16
    DNA2.0 Custom Variant and Variant Library Synthesis for SLC6A16

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607972    OMIM disorders: --

    1 disease for SLC6A16:    
    About MalaCards
    prostatitis


    SLC6A16 for disorders           About GeneDecksing


    Export disorders for SLC6A16 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SLC6A16 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SLC6A16)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning and characterization of human NTT5 and v7-3: two orphan transporters of the Na(+)/Cl(-)-dependent neurotransmitter transporter gene family. (PubMed id 11112352)1, 2, 3 Farmer M.K.... Pangalos M.N. (Genomics 2000)
    2. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (Genome Res. 2001)
    3. Neurotransmitter transporters in the central nervous system. (PubMed id 10471414)1, 3 Masson J....El Mestikawy S. (Pharmacol. Rev. 1999)
    4. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. (PubMed id 21248752)2 Varela I....Futreal P.A. (Nature 2011)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    6. (PubMed id )2 

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
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      Query String
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 28968 HGNC: 13622 AceView: SLC6A16 Ensembl:ENSG00000063127 euGenes: HUgn28968
    ECgene: SLC6A16 H-InvDB: SLC6A16

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SLC6A16 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SLC6A16 gene:
    Search GeneIP for patents involving SLC6A16

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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