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SLC10A4 Gene

protein-coding   GIFtS: 49
GCID: GC04P048485

Solute Carrier Family 10, Member 4

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(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 10, Member 41 2     Sodium/Bile Acid Cotransporter 42
Na(+)/Bile Acid Cotransporter 42 3     Solute Carrier Family 10 (Sodium/Bile Acid Cotransporter Family), Member 42
P42     Solute Carrier Family 10 Member 43
Bile Acid Transporter SLC10A42     

External Ids:    HGNC: 229801   Entrez Gene: 2017802   Ensembl: ENSG000001452487   UniProtKB: Q96EP93   

Export aliases for SLC10A4 gene to outside databases

Previous GC identifers: GC04P048335 GC04P048400 GC04P048326 GC04P048180 GC04P047805


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SLC10A4 Gene:
SLC10A4 (solute carrier family 10, member 4) is a protein-coding gene. GO annotations related to this gene include bile acid:sodium symporter activity. An important paralog of this gene is SLC10A3.


(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 at NCBI GenBank:
NC_000004.11  NC_018915.2  NT_006238.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the SLC10A4 gene promoter:
         Max1   AML1a   HOXA3   Evi-1   HNF-1A   FAC1   HFH-1   HNF-1   MRF-2   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSLC10A4 promoter sequence
   Search Chromatin IP Primers for SLC10A4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLC10A4


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

Entrez Gene cytogenetic band: 4p11   Ensembl cytogenetic band:  4p11   HGNC cytogenetic band: 4p12

SLC10A4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC10A4 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P048485:  view genomic region     (about GC identifiers)

Start:
48,485,360 bp from pter      End:
48,491,541 bp from pter
Size:
6,182 bases      Orientation:
plus 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: NTCP4_HUMAN, Q96EP9 (See protein sequence)
Recommended Name: Sodium/bile acid cotransporter 4  
Size: 437 amino acids; 46504 Da
Secondary accessions: Q8WUZ2

Explore the universe of human proteins at neXtProt for SLC10A4: NX_Q96EP9

Explore proteomics data for SLC10A4 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys407
  • Glycosylation2 at Asn6, Asn18, Asn24
  • Modification sites at PhosphoSitePlus

  • See SLC10A4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689892.1  
    ENSEMBL proteins: 
     ENSP00000273861  

    SLC10A4 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for SLC10A4

     
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    Cloud-Clone Corp. ELISAs for SLC10A4
    Cloud-Clone Corp. CLIAs for SLC10A4
    Search eBioscience for ELISAs for SLC10A4 


    (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: Sodium/bile acid cotransporter 4
    SLC10 family of sodium-bile acid co-transporters

    1 InterPro protein domain:
     IPR002657 BilAc/Na_symport

    Graphical View of Domain Structure for InterPro Entry Q96EP9

    ProtoNet protein and cluster: Q96EP9

    1 Blocks protein domain: IPB002657 Bile acid:sodium symporter

    UniProtKB/Swiss-Prot: NTCP4_HUMAN, Q96EP9
    Similarity: Belongs to the bile acid:sodium symporter (BASS) (TC 2.A.28) family


    Find genes that share domains with SLC10A4           About GenesLikeMe


    (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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008508bile acid:sodium symporter activity IEA--
         
    Find genes that share ontologies with SLC10A4           About GenesLikeMe


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Slc10a4):
     behavior/neurological  nervous system 

    Find genes that share phenotypes with SLC10A4           About GenesLikeMe

    Animal Models:
         MGI mouse knock-out Slc10a4tm1Tigm for SLC10A4

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SLC10A4
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    miRNA
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    7 qRT-PCR Assays for microRNAs that regulate SLC10A4:
    hsa-miR-140-3p hsa-miR-576-5p hsa-miR-205* hsa-miR-26a hsa-miR-4263 hsa-miR-26b hsa-miR-1297
    SwitchGear 3'UTR luciferase reporter plasmidSLC10A4 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SLC10A4

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    GenScript: all cDNA clones in your preferred vector: SLC10A4 (NM_152679)
    Browse Sino Biological Human cDNA Clones
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC10A4


    (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
    NTCP4_HUMAN, Q96EP9: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    cytosol1
    nucleus1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with SLC10A4           About GenesLikeMe


    (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 SLC10A4
    Interactions:

        Search GeneGlobe Interaction Network for SLC10A4

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

    2 Interacting proteins for SLC10A4 (ENSP000002738614) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBCENSP000003448184STRING: ENSP00000344818
    NIP7ENSP000002549404STRING: ENSP00000254940
    About this table

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006814sodium ion transport ----

    Find genes that share ontologies with SLC10A4           About GenesLikeMe



    (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 SLC10A4 (NTCP4)

    1 HMDB Compound for SLC10A4    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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SLC10A4 gene: 
    NM_152679.3  

    Unigene Cluster for SLC10A4:

    Solute carrier family 10 (sodium/bile acid cotransporter family), member 4
    Hs.132591  [show with all ESTs]
    Unigene Representative Sequence: NM_152679
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000273861(uc003gyc.2)
    miRNA
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    7 qRT-PCR Assays for microRNAs that regulate SLC10A4:
    hsa-miR-140-3p hsa-miR-576-5p hsa-miR-205* hsa-miR-26a hsa-miR-4263 hsa-miR-26b hsa-miR-1297
    SwitchGear 3'UTR luciferase reporter plasmidSLC10A4 3' UTR sequence
    Inhib. RNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat SLC10A4
      QuantiFast Probe-based Assays in human, mouse, rat SLC10A4

    Additional mRNA sequence: 

    AK126542.1 AY704414.1 BC012048.1 BC019066.2 

    2 DOTS entries:

    DT.97762654  DT.100716078 

    20 AceView cDNA sequences:

    BC019066 AK126542 BX369076 BF312464 AI418669 AI421729 NM_152679 BC012048 
    BE439690 BE439637 BE260783 AL522530 AA776274 AI031855 AI421796 BI198043 
    AL563624 AL530028 AL522529 BU940291 

    GeneLoc Exon Structure


    (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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    SLC10A4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAACAATTCT
    SLC10A4 Expression
    About this image


    SLC10A4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Brain (Nervous System)    fully expand to see all 19 entries
             Thalamus
             Septum   
     
     Neural Tube (Nervous System)    fully expand to see all 4 entries
             Telencephalon
             brain/midbrain/lateral wall   
     
     Neurons
             Cholinergic Amacrine Cells Inner Nuclear Layer
     
     Eye (Sensory Organs)
             Cholinergic Amacrine Cells Inner Nuclear Layer
     
     Spinal Cord (Nervous System)
    SLC10A4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SLC10A4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.132591
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC10A4

    (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 SLC10A4 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Slc10a41 , 5 solute carrier family 10 (sodium/bile acid cotransporter more1, 5 83.75(n)1
    87.36(a)1
      5 (38.44 cM)5
    2312901  NM_173403.21  NP_775579.21 
     730069045 
    chicken
    (Gallus gallus)
    Aves SLC10A41 solute carrier family 10 (sodium/bile acid cotransporter more 70.02(n)
    71.79(a)
      770263  XM_001233593.3  XP_001233594.2 
    lizard
    (Anolis carolinensis)
    Reptilia SLC10A46
    solute carrier family 10, member 4
    72(a)
    1 ↔ 1
    GL343293.1(868629-877096)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia slc10a41 solute carrier family 10 (sodium/bile acid cotransporter more 69.28(n)
    73.19(a)
      100491322  XM_002933457.2  XP_002933503.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.155802 Transcribed sequence with weak similarity to protein more 75.57(n)    BM316761.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG116556
    CG99036
    --
    15(a)
    14(a)
    many ↔ many
    many ↔ many
    X(15347504-15349584)
    X(16433186-16434885)
    worm
    (Caenorhabditis elegans)
    Secernentea Y71G10AR.46
    Protein Y71G10AR.4 (Y71G10AR.4) mRNA, complete cds...
    15(a)
    1 → many
    IV(2198997-2208831) WBGene00044650


    ENSEMBL Gene Tree for SLC10A4 (if available)
    TreeFam Gene Tree for SLC10A4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SLC10A4 gene
    SLC10A32  SLC10A12  SLC10A62  SLC10A22  SLC10A52  
    3 SIMAP similar genes for SLC10A4 using alignment to 1 protein entry:     NTCP4_HUMAN:
    SLC10A2    SLC10A6    SLC10A1

    Find genes that share paralogs with SLC10A4           About GenesLikeMe



    (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 SLC10A4 (see all 107)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1148462531,2
    F--48483403(+) ACAGGC/AACACA 1 -- us2k11Minor allele frequency- A:0.01WA 118
    rs64476401,2
    C,F,H--48483416(+) ACCATG/ACCCAA 1 -- us2k113Minor allele frequency- A:0.37NA WA CSA EA 378
    rs1928075721,2
    --48483447(+) CCAGAC/TGGGGT 1 -- us2k10--------
    rs1837103601,2
    --48483889(+) GTAACA/GGTTGG 1 -- us2k10--------
    rs76978511,2
    C,F,A,H--48483930(+) TTTCTC/TTTTAC 1 -- us2k1 trp330Minor allele frequency- T:0.45NS EA NA WA CSA 2775
    rs1149778241,2
    F--48483995(+) TAAAGT/ATTAGC 1 -- us2k11Minor allele frequency- A:0.03WA 118
    rs1456241001,2
    --48484014(+) GTTTTC/TTTTTC 1 -- us2k10--------
    rs68129801,2
    C,F,H--48484060(+) TATCCT/GCCTAG 1 -- us2k18Minor allele frequency- G:0.06NS NA WA 1012
    rs778146001,2
    C,F--48484138(+) GAAGAG/ATGCAA 1 -- us2k11Minor allele frequency- A:0.06NA 120
    rs343861021,2
    C,F--48484266(+) GGAGTT/CAGGGA 1 -- us2k110Minor allele frequency- C:0.16NA CSA WA EA 371

    HapMap Linkage Disequilibrium report for SLC10A4 (48485360 - 48491541 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for SLC10A4:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv5542n71CNV Loss21882294
    nsv470034CNV Gain18288195
    nsv829925CNV Gain+Loss17160897

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SLC10A4
    DNA2.0 Custom Variant and Variant Library Synthesis for SLC10A4

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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      --

    (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 SLC10A4 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SLC10A4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    2. SLC10A4 is a protease-activated transporter that transports bile acids. (PubMed id 23589386)1 Abe T....Tomioka Y. (J. Biochem. 2013)
    3. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. (PubMed id 23128233)1 Jostins L....Cho J.H. (Nature 2012)
    4. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    5. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    6. Cloning and expression of SLC10A4, a putative organic anion transport protein. (PubMed id 17106928)1 Splinter P.L....LaRusso N.F. (World J. Gastroenterol. 2006)
    7. The solute carrier family SLC10: more than a family of bile acid transporters regarding function and phylogenetic relationships. (PubMed id 16541252)1 Geyer J....Petzinger E. (Naunyn Schmiedebergs Arch. Pharmacol. 2006)
    8. 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)
    9. (PubMed id )2 
    10. Cloning and molecular characterization of the orphan carrier protein Slc10a4: expression in cholinergic neurons of the rat central nervous system. (PubMed id 18355966)9 Geyer J....Petzinger E. (Neuroscience 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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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: 201780 HGNC: 22980 AceView: SLC10A4 Ensembl:ENSG00000145248 euGenes: HUgn201780
    ECgene: SLC10A4 H-InvDB: SLC10A4

    (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 SLC10A4 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 SLC10A4 gene:
    Search GeneIP for patents involving SLC10A4

    GeneCards and IP:
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