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R3HDM4 Gene

protein-coding   GIFtS: 38
GCID: GC19M000896

R3H Domain Containing 4

(Previous name: chromosome 19 open reading frame 22)
(Previous symbol: C19orf22)
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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
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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 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  NC_018930.2  NT_011295.12  
Regulatory elements:
   Search for regulatory transcription factor binding sites for R3HDM4
         Other transcription factors

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

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 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: R3HD4_HUMAN, Q96D70 (See protein sequence)
Recommended Name: R3H domain-containing protein 4  
Size: 268 amino acids; 30350 Da

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

Explore proteomics data for R3HDM4 at MOPED


See R3HDM4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

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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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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


Find genes that share domains with R3HDM4           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:0003676nucleic acid binding IEA--
     
Find genes that share ontologies with R3HDM4           About GenesLikeMe


Animal Models:
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miRTarBase miRNAs that target R3HDM4:
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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
R3HD4_HUMAN, Q96D70: Nucleus (Potential)

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

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

Find genes that share ontologies with R3HDM4           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 R3HDM4
Interactions:

    Search GeneGlobe Interaction Network for R3HDM4

(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 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,
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 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
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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 

Selected AceView cDNA sequences (see all 264):

CR606082 BM705524 CB215805 BE207399 CR596729 CR616128 CR614470 BM809880 
AW239312 BU607795 CR619216 AA456780 CR597374 CR622307 BE336717 BE207461 
BI820024 BM553385 CR599301 BM462242 CR592767 AI934784 BU185009 BC012775 

GeneLoc Exon Structure

Selected 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™, 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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R3HDM4 expression in normal human tissues (normalized intensities)
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
 
 Bone (Muscoskeletal System)
         Bone Marrow
R3HDM4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

R3HDM4 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.557655
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In Situ
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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 chordates.

Orthologs for R3HDM4 gene from Selected species (see all 9)    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
81.17(n)1
86.64(a)1
  10 (39.72 cM)5
1092841  NM_177994.41  NP_818775.21 
 799100535 
chicken
(Gallus gallus)
Aves R3HDM41 chromosome 28 open reading frame, human C19orf22 71.58(n)
67.73(a)
  770563  XM_001233901.3  XP_001233902.2 
tropical clawed frog
(Xenopus tropicalis)
Amphibia r3hdm41 R3H domain containing 4 62.4(n)
61.05(a)
  779758  NM_001078837.1  NP_001072305.1 
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)
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  --

(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 R3HDM4 (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: --
Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing R3HDM4
DNA2.0 Custom Variant and Variant Library Synthesis for R3HDM4

(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 R3HDM4 gene integrated from 10 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. (Genome Res. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  3. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? (PubMed id 23314748)1 Nathan J.A....Goldberg A.L. (EMBO J. 2013)
  4. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)

(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: 91300 HGNC: 28270 AceView: C19orf22 Ensembl:ENSG00000198858 euGenes: HUgn91300
ECgene: R3HDM4 H-InvDB: R3HDM4

(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 R3HDM4 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 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, 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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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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