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RTBDN Gene

protein-coding   GIFtS: 46
GCID: GC19M012936

Retbindin

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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
retbindin1 2

External Ids:    HGNC: 303101   Entrez Gene: 835462   Ensembl: ENSG000001320267   OMIM: 6095535   UniProtKB: Q9BSG53   

Export aliases for RTBDN gene to outside databases

Previous GC identifers: GC19M013067 GC19M013159 GC19M012781 GC19M012797 GC19M012507


(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 RTBDN Gene:
This gene was first identified in a study of human eye tissues. The protein encoded by this gene is preferentially
expressed in the retina and may play a role in binding retinoids and other carotenoids as it shares homology with
riboflavin binding proteins. Alternative splicing results in multiple transcript variants and protein isoforms.
(provided by RefSeq, Jul 2012)

GeneCards Summary for RTBDN Gene:
RTBDN (retbindin) is a protein-coding gene.




(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_000019.9  NT_011295.12  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RTBDN gene promoter:
         c-Fos   Spz1   AP-1   POU2F1   POU2F1a   Chx10   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): RTBDN promoter sequence
   Search Chromatin IP Primers for RTBDN

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


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

Entrez Gene cytogenetic band: 19p12   Ensembl cytogenetic band:  19p13.2   HGNC cytogenetic band: 19p13

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

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M012936:  view genomic region     (about GC identifiers)

Start:
12,936,292 bp from pter      End:
12,946,242 bp from pter
Size:
9,951 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, 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: RTBDN_HUMAN, Q9BSG5 (See protein sequence)
Recommended Name: Retbindin precursor  
Size: 229 amino acids; 24615 Da
Secondary accessions: F1T0I8 Q9BWT5
Alternative splicing: 3 isoforms:  Q9BSG5-1   Q9BSG5-2   Q9BSG5-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RTBDN: NX_Q9BSG5

Explore proteomics data for RTBDN at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn183

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

    REFSEQ proteins (8 alternative transcripts): 
    NP_001074466.1  NP_001257369.1  NP_001257370.1  NP_001257371.1  NP_001257372.1  NP_001257373.1  NP_001257374.1  NP_113617.1  

    ENSEMBL proteins: 
     ENSP00000466765   ENSP00000468697   ENSP00000326253   ENSP00000416375   ENSP00000464869  
     ENSP00000466382   ENSP00000465796   ENSP00000467888   ENSP00000466855   ENSP00000466805  
     ENSP00000468552   ENSP00000468769   ENSP00000376925  

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    Search eBioscience for ELISAs for RTBDN 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR018143 Folate_rcpt-like
     IPR004269 Folate_rcpt

    Graphical View of Domain Structure for InterPro Entry Q9BSG5

    ProtoNet protein and cluster: Q9BSG5

    UniProtKB/Swiss-Prot: RTBDN_HUMAN, Q9BSG5
    Similarity: Belongs to the folate receptor family


    Find genes that share domains with RTBDN           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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    Phenotypes:
         1 GenomeRNAi human phenotype for RTBDN:
     Decreased nuclei size in G2M 

         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Rtbdn):
     pigmentation  vision/eye 

    Find genes that share phenotypes with RTBDN           About GenesLikeMe

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RTBDN
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for RTBDN
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for RTBDN

    miRNA
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    miRTarBase miRNAs that target RTBDN:
    hsa-mir-335-5p (MIRT018579)

    Block miRNA regulation of human, mouse, rat RTBDN using miScript Target Protectors
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    SwitchGear 3'UTR luciferase reporter plasmidRTBDN 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 2): RTBDN (NM_031429)
    Sino Biological Human cDNA Clone for RTBDN
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RTBDN

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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
    RTBDN_HUMAN, Q9BSG5: Secreted (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular3
    cytosol2
    nucleus2
    plasma membrane1

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region IEA--

    Find genes that share ontologies with RTBDN           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 RTBDN
    Interactions:

        Search GeneGlobe Interaction Network for RTBDN

    (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 RTBDN



    (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 RTBDN gene (8 alternative transcripts): 
    NM_001080997.2  NM_001270440.1  NM_001270441.1  NM_001270442.1  NM_001270443.1  NM_001270444.1  NM_001270445.1  NM_031429.2  

    Unigene Cluster for RTBDN:

    Retbindin
    Hs.21162  [show with all ESTs]
    Unigene Representative Sequence: NM_001270440
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000592204 ENST00000589272 ENST00000322912 ENST00000458671(uc002mvi.3)
    ENST00000586969 ENST00000589681 ENST00000589808 ENST00000590404 ENST00000585384
    ENST00000589567 ENST00000591512 ENST00000587549 ENST00000393233(uc002mvh.1 uc021upo.1 uc002mvj.3)

    miRNA
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    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat RTBDN
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    OriGene ORF clones in mouse, rat for RTBDN
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): RTBDN (NM_031429)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RTBDN
    Primer
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    OriGene qPCR primer pairs and template standards for RTBDN
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat RTBDN
      QuantiTect SYBR Green Assays in human, mouse, rat RTBDN
      QuantiFast Probe-based Assays in human, mouse, rat RTBDN

    Additional mRNA sequence: 

    AB593122.1 AK093672.1 AY028917.1 BC005063.1 

    6 DOTS entries:

    DT.113378  DT.100035995  DT.100035997  DT.95254854  DT.97783367  DT.121485678 

    Selected AceView cDNA sequences (see all 81):

    BU726864 BF026992 BM708463 BQ639040 BM704914 BQ638952 BI753965 BQ638862 
    BU689643 BQ637671 BQ636283 BU730770 AY028917 BM692971 BQ637978 BU732476 
    BC005063 BX281009 AI570570 BQ636938 BU629732 NM_031429 BU726909 BE783827 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for RTBDN (see all 12)    About this scheme

    ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11a · 11b · 11c · 11d · 11e
    SP1:                                -     -     -     -     -                 -                                                               
    SP2:                                -     -     -     -     -                 -                                   -                           
    SP3:                                      -     -     -     -                 -                                   -                           
    SP4:                                      -     -     -     -     -           -                                   -                           
    SP5:                                                  -     -     -           -                                   -                           


    ECgene alternative splicing isoforms for RTBDN

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


    RTBDN expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Eye (Sensory Organs)
             Mature Rod Cells Outer Nuclear Layer
     
     Neurons
             Mature Rod Cells Outer Nuclear Layer
    RTBDN Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RTBDN Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.21162

    UniProtKB/Swiss-Prot: RTBDN_HUMAN, Q9BSG5
    Tissue specificity: Expressed in retina

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    In Situ
    Assay Products:
     

     
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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 human and mouse.

    Orthologs for RTBDN gene from Selected species (see all 5)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rtbdn1 , 5 retbindin1, 5 73.03(n)1
    60.67(a)1
      8 (41.37 cM)5
    2345421  NM_144929.21  NP_659178.11 
     849469915 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RTBDN gene
    Selected SIMAP similar genes for RTBDN using alignment to 11 protein entries:     RTBDN_HUMAN (see all proteins) (see all similar genes):
    AURA2    FKBP3    DCTN5    UTY    ZNF74    ZNF737
    X-linked retinopathy protein    ZNF738    C14orf105    COQ5    OK/SW-cl.41    PLEKHH2
    C3orf64    IDNK    HC6    KIAA1651    LINC00269    ELP4

    Find genes that share paralogs with RTBDN           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for RTBDN
    PGOHUM00000259302


    (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 RTBDN (see all 249)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1408110781,2
    --12935798(+) AGGCAC/TGGGTC 8 -- ds50010--------
    rs2010509261,2
    --12935855(+) TCCTT-/TCTCTCT 8 -- ds50010--------
    rs104151281,2
    C,F--12935881(+) tttgtG/Agagac 8 -- ds50011Minor allele frequency- A:0.14WA 118
    rs348365581,2
    C--12936057(+) GCACA-/CCAGTG 8 -- ds50010--------
    rs48047331,2
    C,F,A,H--12936059(+) CACACA/CGTGGG 8 -- ds50014Minor allele frequency- C:0.07NA WA EA 362
    rs48047341,2
    C,F,A,H--12936060(+) ACACAG/ATGGGA 8 -- ds50011Minor allele frequency- A:0.50NA 4
    rs345894971,2
    C--12936163(+) ACAGG-/CTAT  
            
    CTATC
    8 -- ds50010--------
    rs48047351,2
    C,F,A,H--12936190(+) TATGAG/ATCAGT 8 -- ds500120Minor allele frequency- A:0.07NS EA NA CSA WA 2362
    rs1887533641,2
    --12936239(+) CGTTAC/GTTTCT 8 -- ds50010--------
    rs1497996771,2
    --12936260(+) CTTCCG/TACTTA 8 -- ds50010--------

    HapMap Linkage Disequilibrium report for RTBDN (12936292 - 12946242 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for RTBDN:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv2420CNV Insertion18451855
    nsv911082CNV Loss21882294
    nsv911083CNV Loss21882294
    dgv3733n71CNV Loss21882294

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

    (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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    OMIM gene information: 609553    OMIM disorders: --


    Find genes that share disorders with RTBDN           About GenesLikeMe

    Genetic Association Database (GAD): RTBDN

    Export disorders for RTBDN 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 RTBDN gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with RTBDN)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Expressed sequence tag analysis of human retina for the NEIBank project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. (PubMed id 12107411)1, 2, 3 Wistow G.... Peterson K. (Mol. Vis. 2002)
    2. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. (PubMed id 21697133)1, 2 Oshikawa M.... Kato S. (Invest. Ophthalmol. Vis. Sci. 2011)
    3. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. (PubMed id 19862010)1, 4 Ganesh S.K....Lin J.P. (Nat. Genet. 2009)
    4. 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)
    5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (Genomics 2007)
    6. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (PubMed id 16712791)1 Wang A.G....Kim N.S. (Biochem. Biophys. Res. Commun. 2006)
    7. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
    9. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)2 Grimwood J.... Lucas S.M. (Nature 2004)
    10. 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)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
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      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 83546 HGNC: 30310 AceView: RTBDN Ensembl:ENSG00000132026 euGenes: HUgn83546
    ECgene: RTBDN H-InvDB: RTBDN

    (According to HUGE)
    About This Section

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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)
    About This Section

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    NameDescription
    PharmGKB entry for RTBDN 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 RTBDN gene:
    Search GeneIP for patents involving RTBDN

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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