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SLC4A9 Gene

protein-coding   GIFtS: 48
GCID: GC05P139719

Solute Carrier Family 4, Sodium Bicarbonate Cotransporter,...

  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 4, Sodium Bicarbonate Cotransporter, Member 91 2     Solute Carrier Family 4, Sodium Bicarbonate Cotransporter-Like, Member 92
Anion Exchanger 42 3     SBC53
Sodium Bicarbonate Cotransporter 52 3     AE 43
AE42 3     Solute Carrier Family 4 Member 93
Anion Exchange Protein 42     

External Ids:    HGNC: 110351   Entrez Gene: 836972   Ensembl: ENSG000001130737   OMIM: 6102075   UniProtKB: Q96Q913   

Export aliases for SLC4A9 gene to outside databases

Previous GC identifers: GC05P139556 GC05P140322 GC05P139722 GC05P139768 GC05P134884


(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 SLC4A9 Gene:
The protein encoded by this gene is a membrane protein involved in anion exchange. Expression of this gene is
mostly limited to the kidney. Several transcript variants encoding different isoforms have been found for this
gene. (provided by RefSeq, May 2012)

GeneCards Summary for SLC4A9 Gene:
SLC4A9 (solute carrier family 4, sodium bicarbonate cotransporter, member 9) is a protein-coding gene. Diseases associated with SLC4A9 include hidradenoma. GO annotations related to this gene include inorganic anion exchanger activity. An important paralog of this gene is SLC4A10.

UniProtKB/Swiss-Prot: B3A4_HUMAN, Q96Q91
Function: Probable apical anion exchanger of the kidney cortex (By similarity)




(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_000005.10  NT_029289.12  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SLC4A9 gene promoter:
         ER-alpha   STAT1   STAT1beta   STAT5A   Nkx2-5   GATA-2   STAT1alpha   CREB   FOXC1   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSLC4A9 promoter sequence
   Search Chromatin IP Primers for SLC4A9

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLC4A9


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

Entrez Gene cytogenetic band: 5q31   Ensembl cytogenetic band:  5q31.3   HGNC cytogenetic band: 5q31.3

SLC4A9 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC4A9 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P139719:  view genomic region     (about GC identifiers)

Start:
139,739,787 bp from pter      End:
139,754,728 bp from pter
Size:
14,942 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, 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: B3A4_HUMAN, Q96Q91 (See protein sequence)
Recommended Name: Anion exchange protein 4  
Size: 983 amino acids; 108248 Da
Sequence caution: Sequence=AAK28832.1; Type=Erroneous initiation;
Secondary accessions: B7ZL63 D3DQD4 D3DQD5 D3DQD6 E9PDK1 Q96RM5 Q9BXF2 Q9BXN3
Alternative splicing: 4 isoforms:  Q96Q91-1   Q96Q91-2   Q96Q91-3   Q96Q91-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SLC4A9: NX_Q96Q91

Explore proteomics data for SLC4A9 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn576, Asn600
  • Modification sites at PhosphoSitePlus

  • See SLC4A9 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001245355.1  NP_001245356.1  NP_001245357.1  NP_113655.2  

    ENSEMBL proteins: 
     ENSP00000424424   ENSP00000422855   ENSP00000410056   ENSP00000427661   ENSP00000230993  
    Reactome Protein details: Q96Q91

    SLC4A9 Human Recombinant Protein Products:

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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: Anion exchange protein 4
    Anion exchangers

    5 InterPro protein domains:
     IPR003020 HCO3_transpt_euk
     IPR003024 Na/HCO3_transpt
     IPR011531 HCO3_transpt_C
     IPR016152 PTrfase/Anion_transptr
     IPR013769 Band3_cytoplasmic_dom

    Graphical View of Domain Structure for InterPro Entry Q96Q91

    ProtoNet protein and cluster: Q96Q91

    1 Blocks protein domain: IPB013769 HCO3- transporter

    UniProtKB/Swiss-Prot: B3A4_HUMAN, Q96Q91
    Similarity: Belongs to the anion exchanger (TC 2.A.31) family


    SLC4A9 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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: B3A4_HUMAN, Q96Q91
    Function: Probable apical anion exchanger of the kidney cortex (By similarity)

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005215transporter activity ----
    GO:0005452inorganic anion exchanger activity IEA--
    GO:0008509anion transmembrane transporter activity ----
         
    SLC4A9 for ontologies           About GeneDecksing


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Slc4a9):
     digestive/alimentary  renal/urinary system 

    SLC4A9 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Slc4a9tm1Ges for SLC4A9

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    hsa-miR-22 hsa-miR-875-3p hsa-miR-670 hsa-miR-508-5p hsa-miR-1299
    SwitchGear 3'UTR luciferase reporter plasmidSLC4A9 3' UTR sequence
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    (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
    B3A4_HUMAN, Q96Q91: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    cytosol1
    endoplasmic reticulum1
    peroxisome1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane TAS--
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--
    GO:0045177apical part of cell IEA--

    SLC4A9 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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    SuperPaths for SLC4A9 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
    SLC-mediated transmembrane transport0.47
    Transport of inorganic cations/anions and amino acids/oligopeptides0.38
    Transmembrane transport of small molecules0.47
    Bicarbonate transporters0.00

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for SLC4A9
        Bicarbonate transporters



    SLC4A9 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SLC4A9
    Interactions:

        Search GeneGlobe Interaction Network for SLC4A9

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport ----
    GO:0006811ion transport TAS--
    GO:0006820anion transport ----
    GO:0015701bicarbonate transport TAS--
    GO:0055085transmembrane transport TAS--

    SLC4A9 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 SLC4A9 (B3A4)

    2 Novoseek inferred chemical compound relationships for SLC4A9 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sodium bicarbonate 69.9 1 11305939 (1)
    bicarbonate 68.2 3 12027220 (1), 11302728 (1)



    SLC4A9 for compounds           About GeneDecksing



    (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 SLC4A9 gene (4 alternative transcripts): 
    NM_001258426.1  NM_001258427.1  NM_001258428.1  NM_031467.2  

    Unigene Cluster for SLC4A9:

    Solute carrier family 4, sodium bicarbonate cotransporter, member 9
    Hs.550313  [show with all ESTs]
    Unigene Representative Sequence: NM_001258428
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000506757(uc003lfj.2) ENST00000506545 ENST00000432095 ENST00000507527(uc003lfm.2 uc011czg.1)
    ENST00000514849 ENST00000504742 ENST00000230993(uc003lfl.2 uc003lfk.2)

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    hsa-miR-22 hsa-miR-875-3p hsa-miR-670 hsa-miR-508-5p hsa-miR-1299
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      QuantiFast Probe-based Assays in human, mouse, rat SLC4A9

    Additional mRNA sequence: 

    AB032762.1 AF313465.1 AF332961.1 AF336237.1 BC136262.1 BC143602.1 

    5 DOTS entries:

    DT.99958297  DT.97835984  DT.65286618  DT.75100758  DT.101977341 

    22 AceView cDNA sequences:

    AF313465 CB046220 AI928209 AB032762 AF336237 AA917682 AF332961 NM_031467 
    AW195628 CK002375 CB046221 BX090920 AI498467 AI762331 AW779828 BE048480 
    AI927652 BF197548 AI183992 AW058525 BF826315 AI434423 

    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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    SLC4A9 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTTGCTGTGC
    SLC4A9 Expression
    About this image

    SLC4A9 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SLC4A9 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.550313

    UniProtKB/Swiss-Prot: B3A4_HUMAN, Q96Q91
    Tissue specificity: Kidney specific

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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 SLC4A9 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Slc4a91 , 5 solute carrier family 4, sodium bicarbonate cotransporter, more1, 5 83.82(n)1
    83.26(a)1
      18 (19.46 cM)5
    2402151  NM_001271544.11  NP_001258473.11 
     365281575 
    chicken
    (Gallus gallus)
    Aves SLC4A96
    solute carrier family 4, sodium bicarbonate cotran...
    52(a)
    1 ↔ 1
    13(972298-989098)
    lizard
    (Anolis carolinensis)
    Reptilia SLC4A96
    solute carrier family 4, sodium bicarbonate cotran...
    55(a)
    1 ↔ 1
    4(78058705-78118940)
    fruit fly
    (Drosophila melanogaster)
    Insecta Ndae16
    Na[+]-driven anion exchanger 1
    34(a)
    1 → many
    2L(7223328-7249343)
    worm
    (Caenorhabditis elegans)
    Secernentea abts-16
    Protein ABTS-1, isoform a (abts-1) mRNA, complete ...
    31(a)
    1 → many
    I(8296917-8307566) WBGene00009920


    ENSEMBL Gene Tree for SLC4A9 (if available)
    TreeFam Gene Tree for SLC4A9 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SLC4A9 gene
    SLC4A102  SLC4A72  SLC4A42  SLC4A112  SLC4A12  SLC4A52  SLC4A82  SLC4A22  
    SLC4A32  
    9 SIMAP similar genes for SLC4A9 using alignment to 1 protein entry:     B3A4_HUMAN:
    SLC4A4    SLC4A7    SLC4A10    NBC    SLC4A5    SLC4A8
    SLC4A1    SLC4A2    SLC4A3

    SLC4A9 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 SLC4A9 (see all 391)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1135852291,2
    C--134883186(+) AAAAAG/AAAAGA 4 -- us2k11Minor allele frequency- A:0.50NA 2
    rs1488674231,2
    --134883274(+) TGTAAC/GGATAT 4 -- us2k10--------
    rs623851851,2
    F--134883436(+) CAGGGC/TGTGAA 4 -- us2k11Minor allele frequency- T:0.50NA 2
    rs1435617241,2
    --134883508(+) TGTGTA/TGGGTG 4 -- us2k10--------
    rs1162030661,2
    F--134883510(+) TGTTGG/AGTGAG 4 -- us2k11Minor allele frequency- A:0.05WA 118
    rs1480476901,2
    --134883577(+) GGAGGA/GTGGAC 4 -- us2k10--------
    rs1863433171,2
    --134883749(+) AACAGA/GATTTG 4 -- us2k10--------
    rs764202541,2
    --134883779(+) TCCTTC/TGCTCA 4 -- us2k10--------
    rs1149152831,2
    C,F--134883942(+) CTTACG/CCTTGT 4 -- us2k11Minor allele frequency- C:0.02WA 118
    rs1460416461,2
    C--134883958(+) TAGCAC/TTTTGG 4 -- us2k10--------

    HapMap Linkage Disequilibrium report for SLC4A9 (139739787 - 139754728 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for SLC4A9:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2659425CNV Deletion23128226
    nsv509090CNV Insertion20534489

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SLC4A9
    DNA2.0 Custom Variant and Variant Library Synthesis for SLC4A9

    (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: 610207    OMIM disorders: --

    1 disease for SLC4A9:    About MalaCards
    hidradenoma


    SLC4A9 for disorders           About GeneDecksing


    Export disorders for SLC4A9 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 SLC4A9 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SLC4A9)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31. (PubMed id 11305939)1, 2, 3, 9 Lipovich L.... King M.-C. (Genome Biol. 2001)
    2. Human BTR1, a new bicarbonate transporter superfamily member and human AE4 from kidney. (PubMed id 11302728)1, 2, 9 Parker M.D.... Tanner M.J.A. (Biochem. Biophys. Res. Commun. 2001)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (Nature 2004)
    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. Na+:HCO3- cotransporters (NBC): expression and regulation in the kidney. (PubMed id 12027220)9 Soleimani M. (J. Nephrol. 2002)
    7. Functional and molecular properties of Na+:HCO-3 cotransporters (NBC). (PubMed id 12847417)9 Soleimani M. (Minerva Urol Nefrol 2003)
    8. Na+:HCO(3-) cotransporters (NBC): cloning and characterization. (PubMed id 11562789)9 Soleimani M. and Burnham C.E. (J. Membr. Biol. 2001)

    (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: 83697 HGNC: 11035 AceView: SLC4A9 Ensembl:ENSG00000113073 euGenes: HUgn83697
    ECgene: SLC4A9 H-InvDB: SLC4A9

    (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 SLC4A9 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 SLC4A9 gene:
    Search GeneIP for patents involving SLC4A9

    GeneCards and IP:
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