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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

R3HDM4 Gene

protein-coding   GIFtS: 38
GCID: GC19M000896

R3H Domain Containing 4

(Previous name: chromosome 19 open reading frame 22)
(Previous symbol: C19orf22)
  Search for R3HDM4
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
R3H Domain Containing 41 2
C19orf221 2 3
Chromosome 19 Open Reading Frame 221
R3H Domain-Containing Protein 42
R3H Domain-Containing Protein C19orf222

External Ids:    HGNC: 282701   Entrez Gene: 913002   Ensembl: ENSG000001988587   UniProtKB: Q96D703   

Export aliases for R3HDM4 gene to outside databases


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for R3HDM4 Gene: 
R3HDM4 (R3H domain containing 4) is a protein-coding gene. GO annotations related to this gene include nucleic acid binding.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000019.9  NC_018930.2  NT_011255.14  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for R3HDM4
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for R3HDM4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat R3HDM4


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

Entrez Gene cytogenetic band: 19p13.3   Ensembl cytogenetic band:  19p13.3   HGNC cytogenetic band: 19p13.3

R3HDM4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
R3HDM4 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M000896:  view genomic region     (about GC identifiers)

Start:
896,503 bp from pter      End:
913,240 bp from pter
Size:
16,738 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: R3HD4_HUMAN, Q96D70 (See protein sequence)
Recommended Name: R3H domain-containing protein 4  
Size: 268 amino acids; 30350 Da
Subcellular location: Nucleus (Potential)

Explore the universe of human proteins at neXtProt for R3HDM4: NX_Q96D70

Explore proteomics data for R3HDM4 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q96D70

  • R3HDM4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    R3HDM4 Protein Expression
    REFSEQ proteins: NP_620129.2  
    ENSEMBL proteins: 
     ENSP00000355385   ENSP00000466823   ENSP00000464744   ENSP00000468026   ENSP00000466124  
     ENSP00000468088  

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    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    R3HDM4 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    2 InterPro protein domains:
     IPR001374 R3H_ss-bd
     IPR025952 R3H-assoc_dom

    Graphical View of Domain Structure for InterPro Entry Q96D70

    ProtoNet protein and cluster: Q96D70

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

    UniProtKB/Swiss-Prot: R3HD4_HUMAN, Q96D70
    Similarity: Contains 1 R3H domain


    R3HDM4 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
         
    R3HDM4 for ontologies           About GeneDecksing


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    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section




    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for R3HDM4

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for R3HDM4 (R3HD4)

    Search CenterWatch for drugs/clinical trials and news about R3HDM4 / R3HD4

    (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,
    RNAi Products from EMD Millipore,
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    About This Section

    REFSEQ mRNAs for R3HDM4 gene: 
    NM_138774.3  

    Unigene Cluster for R3HDM4:

    R3H domain containing 4
    Hs.557655  [show with all ESTs]
    Unigene Representative Sequence: NM_138774
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000361574(uc002lqg.2) ENST00000589428 ENST00000587975 ENST00000586080
    ENST00000590454 ENST00000591829 ENST00000590259 ENST00000589445
    miRNA
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    Inhib. RNA
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    Additional mRNA sequence: 

    AK000263.1 AK024622.1 

    9 DOTS entries:

    DT.97845591  DT.456358  DT.100782498  DT.95088837  DT.100834608  DT.75103121  DT.86851945  DT.95337198 
    DT.92440012 

    24/264 AceView cDNA sequences (see all 264):

    BE302484 BM705524 CR599301 CB215805 CR622307 BQ015838 BI908462 CR616662 
    BI820024 BM462242 BU185009 BQ674982 AI934784 CR597374 CA308549 AL135100 
    CR615271 BM665704 BE207461 CD243820 CR606082 CR614470 CR592767 CR624510 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for R3HDM4 (see all 7)    About this scheme

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


    ECgene alternative splicing isoforms for R3HDM4

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    R3HDM4 expression in normal human tissues (normalized intensities)      R3HDM4 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGGTCCTCC
    R3HDM4 Expression
    About this image


    R3HDM4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/4 selected tissues (see all 4) fully expand
     
     Blood (Hematopoietic System)    fully expand to see all 2 entries
             umbilical cord reticulocytes   
     
     Umbilical Cord (Extraembryonic Tissues)
             umbilical cord reticulocytes   
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Skeletal Muscle (Muscoskeletal System)
             gastrocnemius muscle   

    See R3HDM4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for R3HDM4

    SOURCE GeneReport for Unigene cluster: Hs.557655
        SABiosciences Custom PCR Arrays for R3HDM4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for R3HDM4

    (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)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for R3HDM4 gene from 3/8 species (see all 8)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia R3hdm41 , 5 RIKEN cDNA C030046I01 gene5
    R3H domain containing 41
    81.23(n)1
    86.97(a)1
      10 (39.72 cM)5
    1092841  NM_177994.41  NP_818775.21 
     799100535 
    chicken
    (Gallus gallus)
    Aves C28H19orf221 chromosome 28 open reading frame, human C19orf22 71.58(n)
    67.73(a)
      770563  XM_001233901.2  XP_001233902.2 
    zebrafish
    (Danio rerio)
    Actinopterygii r3hdm41 R3H domain containing 4 58.4(n)
    55.46(a)
      791165  NM_001080647.1  NP_001074116.1 


    ENSEMBL Gene Tree for R3HDM4 (if available)
    TreeFam Gene Tree for R3HDM4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
      --

    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/520 SNPs in R3HDM4 are shown (see all 520)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1888244061,2
    --896062(+) TGGGAA/TTACAG 1 -- int10--------
    rs1813154061,2
    --896096(+) CCAACC/GCTGCT 1 -- int10--------
    rs1407398581,2
    --896176(+) CAAGCG/TATCCT 1 -- int10--------
    rs29652871,2
    C,F,A,H--896244(-) tgaaaC/Tgacag 1 -- int123Minor allele frequency- T:0.39NS EA NA WA CSA 2340
    rs742534461,2
    C,F--896295(+) CACTCG/ATACAA 1 -- int11Minor allele frequency- A:0.03EA 120
    rs1438090791,2
    C--896333(+) CCAAGA/GCACTC 1 -- int10--------
    rs1415332691,2
    C--896358(+) CCCAA-/GGGTCA 1 -- int10--------
    rs29652861,2
    C,F,A,H--896499(-) GCCTCG/AGGCTA 1 -- int119Minor allele frequency- A:0.14NS EA NA WA CSA 2003
    rs29652851,2
    C--896506(-) TGCTCT/CGGCCT 1 -- ut312Minor allele frequency- C:0.12NA 122
    rs766878131,2
    F--896633(+) GGGACA/GCAGGA 1 -- ut311Minor allele frequency- G:0.01WA 118

    HapMap Linkage Disequilibrium report for R3HDM4 (896503 - 913240 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for R3HDM4: --
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing R3HDM4
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    (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.)
    About This Section
      --

    (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)
    About This Section

    PubMed articles for R3HDM4 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with R3HDM4)
        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. (2004)
    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. (2002)
    3. Why do cellular proteins linked to K63-polyubiquitin c hains not associate with proteasomes? (PubMed id 23314748)1 Nathan J.A....Goldberg A.L. (2013)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 91300 HGNC: 28270 AceView: C19orf22 Ensembl:ENSG00000198858 euGenes: HUgn91300
    ECgene: R3HDM4 H-InvDB: R3HDM4

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for R3HDM4 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for R3HDM4 gene:
    Search GeneIP for patents involving R3HDM4

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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