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R3HCC1 Gene

protein-coding   GIFtS: 46
GCID: GC08P023127

R3H Domain And Coiled-Coil Containing 1

  Search for R3HCC1
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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
R3H Domain And Coiled-Coil Containing 11 2
R3H And Coiled-Coil Domain-Containing Protein 12

External Ids:    HGNC: 273291   Entrez Gene: 2030692   Ensembl: ENSG000001046797   UniProtKB: Q9Y3T63   
ORGUL members:         

Export aliases for R3HCC1 gene to outside databases

Previous GC identifers: GC08P023202 GC08P021691


(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 R3HCC1 Gene:
R3HCC1 (R3H domain and coiled-coil containing 1) is a protein-coding gene. GO annotations related to this gene include nucleotide binding and nucleic acid binding. An important paralog of this gene is R3HCC1L.


(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_000008.11  NT_167187.2  NC_018919.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the R3HCC1 gene promoter:
         HOXA9B   HOXA9   E2F-3a   E2F-4   E2F-5   Pax-6   E2F-2   E2F-1   E2F   Meis-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for R3HCC1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat R3HCC1


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

Entrez Gene cytogenetic band: 8p21.3   Ensembl cytogenetic band:  8p21.3   HGNC cytogenetic band: 8p21.3

R3HCC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
R3HCC1 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08P023127:  view genomic region     (about GC identifiers)

Start:
23,127,633 bp from pter      End:
23,153,792 bp from pter
Size:
26,160 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: R3HC1_HUMAN, Q9Y3T6 (See protein sequence)
Recommended Name: R3H and coiled-coil domain-containing protein 1  
Size: 480 amino acids; 53259 Da
Sequence caution: Sequence=CAB43396.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Cloning
artifact and potential poly-A sequence;
Secondary accessions: B7ZLI1
Alternative splicing: 2 isoforms:  Q9Y3T6-1   Q9Y3T6-2   

Explore the universe of human proteins at neXtProt for R3HCC1: NX_Q9Y3T6

Explore proteomics data for R3HCC1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See R3HCC1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001129580.1  
    ENSEMBL proteins: 
     ENSP00000430607   ENSP00000265806   ENSP00000429417   ENSP00000429604   ENSP00000428395  
     ENSP00000430339   ENSP00000397555  

    R3HCC1 Human Recombinant Protein Products:

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    LSBio Antibodies in human, mouse, rat for R3HCC1

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    Cloud-Clone Corp. CLIAs for R3HCC1


    (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:
     IPR001374 R3H_ss-bd
     IPR012677 Nucleotide-bd_a/b_plait

    Graphical View of Domain Structure for InterPro Entry Q9Y3T6

    ProtoNet protein and cluster: Q9Y3T6

    1 Blocks protein domain: IPB001374 Single-stranded nucleic acid binding R3H

    UniProtKB/Swiss-Prot: R3HC1_HUMAN, Q9Y3T6
    Similarity: Contains 1 R3H domain


    R3HCC1 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:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding IEA--
         
    R3HCC1 for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for R3HCC1
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    miRNA
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    Predesigned siRNA for gene silencing in human, mouse, rat R3HCC1

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    Browse Sino Biological Human cDNA Clones
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for R3HCC1


    (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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2

    (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 R3HCC1
    Interactions:

        Search GeneGlobe Interaction Network for R3HCC1

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for R3HCC1 (Q9Y3T63 ENSP000002658064) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPP2R2BQ000053, ENSP000003365914I2D: score=1 STRING: ENSP00000336591
    SSBP1ENSP000002653044STRING: ENSP00000265304
    TSFMENSP000003883304STRING: ENSP00000388330
    About this table

    (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 R3HCC1 (R3HC1)



    (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 R3HCC1 gene: 
    NM_001136108.1  

    Unigene Cluster for R3HCC1:

    R3H domain and coiled-coil containing 1
    Hs.458644  [show with all ESTs]
    Unigene Representative Sequence: NM_001136108
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000517633 ENST00000522012 ENST00000518454 ENST00000265806(uc003xdf.3 uc011kzt.2)
    ENST00000519952 ENST00000518840 ENST00000521588 ENST00000520480 ENST00000523720
    ENST00000411463
    miRNA
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    GenScript: all cDNA clones in your preferred vector: R3HCC1 (NM_001136108)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for R3HCC1
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat R3HCC1
    Primer
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    OriGene qPCR primer pairs and template standards for R3HCC1
    OriGene qSTAR qPCR primer pairs in human, mouse for R3HCC1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat R3HCC1
      QuantiTect SYBR Green Assays in human, mouse, rat R3HCC1
      QuantiFast Probe-based Assays in human, mouse, rat R3HCC1

    Additional mRNA sequence: 

    AK293465.1 AL050297.1 BC032421.1 BC050572.1 BC128545.1 BC128546.1 BC143822.1 BC143827.1 
    BC143829.1 

    12 DOTS entries:

    DT.91764468  DT.100698776  DT.75102174  DT.121478637  DT.91764467  DT.100790011  DT.91785317  DT.95099656 
    DT.97845456  DT.100849179  DT.40274550  DT.97845454 

    Selected AceView cDNA sequences (see all 196):

    CR600229 CR590969 BG820589 CR591686 CA309685 CR605355 CR610879 BQ278756 
    CR602549 AL527168 CR605793 AL518119 CR617722 AL521715 BF133557 BG818561 
    BM694064 CR591817 CR626128 BI770649 BE298678 AI962231 BE298874 BM785376 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for R3HCC1 (see all 6)    About this scheme

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


    ECgene alternative splicing isoforms for R3HCC1

    (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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    R3HCC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGGTGTGGTG
    R3HCC1 Expression
    About this image

    R3HCC1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    R3HCC1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.458644
        Custom PCR Arrays for R3HCC1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for R3HCC1

    (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 R3HCC1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia R3hcc15 R3H domain and coiled-coil containing 1   --   14 (36.08 cM) 69697307 
    chicken
    (Gallus gallus)
    Aves R3HCC16
    R3H domain and coiled-coil containing 1
    23(a)
    1 ↔ 1
    22(1240998-1250082)
    lizard
    (Anolis carolinensis)
    Reptilia R3HCC16
    R3H domain and coiled-coil containing 1
    21(a)
    1 ↔ 1
    GL343679.1(17518-27573)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.193482 Xenopus laevis transcribed sequence with weak similarity more 74.28(n)    BJ073354.1 
    zebrafish
    (Danio rerio)
    Actinopterygii r3hcc16
    R3H domain and coiled-coil containing 1
    15(a)
    1 ↔ 1
    10(20426572-20482737) ENSDARG00000088146
    fruit fly
    (Drosophila melanogaster)
    Insecta CG21626
    --
    11(a)
    1 → many
    3L(3035196-3040469)


    ENSEMBL Gene Tree for R3HCC1 (if available)
    TreeFam Gene Tree for R3HCC1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for R3HCC1 gene
    R3HCC1L2  
    2 SIMAP similar genes for R3HCC1 using alignment to 5 protein entries:     R3HC1_HUMAN (see all proteins):
    R3HCC1L    C10orf28

    R3HCC1 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 R3HCC1 (see all 268)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1412869271,2
    C--23143661(+) TTCTT-/TTTC  
            
    TTTCT
    1 -- us2k10--------
    rs786779871,2
    --23143694(+) TTTCTC/TTCTTT 1 -- us2k10--------
    rs1859982201,2
    C--23143760(+) TGCATA/TTACTC 1 -- us2k10--------
    rs759671811,2
    F--23143888(+) GGAGAC/TCTGGA 1 -- us2k12Minor allele frequency- T:0.05WA NA 238
    rs1911615291,2
    --23143889(+) GAGACC/TTGGAC 1 -- us2k10--------
    rs1818892301,2
    --23144011(+) AATTTG/TTTGAA 1 -- us2k10--------
    rs1854960861,2
    --23144135(+) CCTCTC/GTTTTC 1 -- us2k10--------
    rs1492146371,2
    --23144184(+) CCTCAC/TGCTGC 1 -- us2k10--------
    rs48721011,2
    C,F,A,H--23144234(+) TGTGGT/CCTGCT 1 -- us2k111Minor allele frequency- C:0.35NA CSA WA EA 376
    rs1433574791,2
    --23144250(+) TTCCAA/TTAAGC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for R3HCC1 (23127633 - 23153792 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for R3HCC1: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing R3HCC1
    DNA2.0 Custom Variant and Variant Library Synthesis for R3HCC1

    (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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    R3HCC1 for disorders           About GeneDecksing

    Genetic Association Database (GAD): R3HCC1
    Human Genome Epidemiology (HuGE) Navigator: R3HCC1 (1 document)

    Export disorders for R3HCC1 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 R3HCC1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with R3HCC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Efficacy of metformin therapy in adolescent girls with androgen excess: relation to sex hormone-binding globulin and androgen receptor polymorphisms. (PubMed id 20691435)1, 4 DA-az M....IbA!A+ez L. (Fertil. Steril. 2010)
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    3. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    4. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    5. DNA sequence and analysis of human chromosome 8. (PubMed id 16421571)2 Nusbaum C....Lander E.S. (Nature 2006)
    6. 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)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      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: 203069 HGNC: 27329 AceView: LOC203069 Ensembl:ENSG00000104679 euGenes: HUgn203069
    ECgene: R3HCC1 H-InvDB: R3HCC1

    (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 R3HCC1 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 R3HCC1 gene:
    Search GeneIP for patents involving R3HCC1

    GeneCards and IP:
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    (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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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