R3HDM1 Gene
protein-coding GIFtS: 48
GCID: GC02P136289
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|
R3H domain containing 1(Previous name: R3H domain (binds single-stranded nucleic acids) containing...)
(Previous symbol: R3HDM)
| |
Aliases
for R3HDM1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| R3H Domain Containing 11 2 | | R3HDM1 2 3 | | R3H Domain (Binds Single-Stranded Nucleic Acids) Containing1 2 | | KIAA00291 3 | | R3H Domain-Containing Protein 12 |
Export aliases for R3HDM1 gene to outside databasesPrevious GC identifers: GC02P136123 GC02P136005 GC02P128281 |
Summaries
for R3HDM1 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
-- |
Genomic Views
for R3HDM1 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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000002.11 NC_018913.1 NT_022135.16
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the R3HDM1 gene promoter:
USF1 AP-2alpha isoform 3 Tal-1 AML1a p300 AP-2alpha isoform 2 E47 USF-1 AP-2alpha isoform 4 AP-2alpha
Other transcription factors
Search SABiosciences Chromatin IP Primers for R3HDM1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat R3HDM1 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 2q21.3 Ensembl cytogenetic band: 2q21.3 HGNC cytogenetic band: 2q21.3R3HDM1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 2 GeneLoc Exon Structure GeneLoc location for GC02P136289: view genomic region
(about GC identifiers)
Start:
|
136,289,025 bp from pter |
End:
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136,482,840 bp from pter |
Size:
|
193,816 bases |
Orientation:
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plus strand |
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Proteins
for R3HDM1 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
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
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: R3HD1_HUMAN, Q15032 (See
protein sequence)Recommended Name: R3H domain-containing protein 1 Size: 1099 amino acids; 120696 Da
Sequence caution: Sequence=BAA04878.2; Type=Erroneous initiation;
Secondary accessions: Q8IW32Alternative splicing: 2 isoforms: Q15032-1 Q15032-2 Explore the universe of human proteins at neXtProt for R3HDM1: NX_Q15032
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q15032
R3HDM1 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_056176.2
ENSEMBL proteins: ENSP00000386457 ENSP00000264160 ENSP00000404098 ENSP00000386877 ENSP00000416082 ENSP00000387010 ENSP00000405668 ENSP00000402940 ENSP00000403406 ENSP00000387750 ENSP00000413763 ENSP00000331396
Human Recombinant Protein Products:
R3HDM1 Antibody Products:
Assay Products for R3HDM1: |
Protein
Domains /
Families
for R3HDM1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
R3HDM1 for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q15032ProtoNet protein and cluster: Q15032 1 Blocks protein family: IPB001374 Single-stranded nucleic acid binding R3H
UniProtKB/Swiss-Prot: R3HD1_HUMAN, Q15032Similarity: Contains 1 R3H domainSimilarity: Contains 1 SUZ domain |
Function
for R3HDM1 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
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,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for R3HDM1 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for R3HDM1
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: R3HDM1 (NM_015361) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for R3HDM1 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat R3HDM1 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for R3HDM1 |
Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0003676 | nucleic acid binding |
IEA | -- |
R3HDM1 for ontologies About GeneDecksing
|
Pathways & Interactions
for R3HDM1 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
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 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for R3HDM1
STRING Interaction
Network Preview (showing 1 interactants - click image to see more details)
3 Interacting proteins for R3HDM1 (Q150322, 3 ENSP000002641604) via UniProtKB, MINT, STRING, and/or I2DAbout this table
|
Drugs & Compounds
for R3HDM1 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for R3HDM1
Search CenterWatch for drugs/clinical trials and news about R3HDM1 / R3HD1
|
Transcripts
for R3HDM1 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 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,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for R3HDM1 gene: NM_015361.2 Unigene Cluster for R3HDM1: R3H domain containing 1 Hs.412462 [show with all ESTs]Unigene Representative Sequence: NM_01536118/20 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 20): ENST00000483021 ENST00000463230 ENST00000409478 ENST00000264160(uc002tuo.3 uc010fni.3)
ENST00000438014 ENST00000488035 ENST00000410054(uc002tup.3 uc010zbh.2)
ENST00000436436 ENST00000409606 ENST00000456040 ENST00000480793 ENST00000486532
ENST00000443537 ENST00000441871 ENST00000429703 ENST00000425804 ENST00000487294
ENST00000445855
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for R3HDM1 (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for R3HDM1
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: R3HDM1 (NM_015361) | | | DNA2.0 Custom Codon Optimized Gene
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Additional cDNA sequence: AK026987.1 AK127793.1 AK290015.1 AK297000.1 BC001217.1 BC041093.1 D21852.1 19 DOTS entries: DT.99936451 DT.444093 DT.97842133 DT.91765962 DT.91765965 DT.120981929 DT.120981938 DT.91765960 DT.99994573 DT.100023489 DT.100783632 DT.120981932 DT.120981978 DT.91937103 DT.92434780 DT.95275633 DT.99959947 DT.120982014 DT.91765963 24/189 AceView cDNA sequences (see all 189): F09566 AI150121 BM984783 AA504206 AI802737 AI983468 AA514884 AW949493 BQ011745 BX477821 AI419397 AW188798 BF437676 AA832377 AI420384 BE856664 AU123526 BM550883 BC041093 CK820227 BM263173 CD557193 BM142469 AA372108
GeneLoc Exon Structure
5/17 Alternative Splicing Database (ASD) splice patterns (SP) for R3HDM1 (see all 17) About this scheme
| ExUns: | 1a | · | 1b | · | 1c | ^ | 2 | ^ | 3 | ^ | 4a | · | 4b | ^ | 5a | · | 5b | · | 5c | · | 5d | ^ | 6a | · | 6b | · | 6c | ^ | 7 | ^ | 8a | · | 8b | ^ | 9a | · | 9b | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13 | ^ | 14 | ^ | 15 | ^ | 16 | ^ |
|---|
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| SP1: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP3: | | | | | | | - | | - | | - | | - | | | | | | | | | | | | - | | - | | - | | - | | - | | | | | | | | | | | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | | | | | | | | | - | | - | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| ExUns: | 17a | · | 17b | ^ | 18a | · | 18b | ^ | 19a | · | 19b | · | 19c | ^ | 20 | ^ | 21 | ^ | 22 | ^ | 23 | ^ | 24 | ^ | 25 | ^ | 26 | ^ | 27 | ^ | 28 |
|---|
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| SP1: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | - | | - | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP3: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | - | | - | | | | | | | | | | | | | | | | | | | | | | | | | |
ECgene alternative splicing isoforms for R3HDM1
|
Expression
for R3HDM1 gene
(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
| R3HDM1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --
About this image
See R3HDM1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for R3HDM1
SOURCE GeneReport for Unigene cluster: Hs.412462
SABiosciences Custom PCR Arrays for R3HDM1
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for R3HDM1
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat R3HDM1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat R3HDM1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat R3HDM1 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for R3HDM1 |
Orthologs
for R3HDM1 gene
(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 eukaryotes.
Orthologs for R3HDM1 gene from 8/23 species (see all 23) About this table
ENSEMBL Gene Tree for R3HDM1 (if available)
TreeFam Gene Tree for R3HDM1 (if available) |
Paralogs
for R3HDM1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for R3HDM1 gene
- R3HDM22 ARPP212
3 SIMAP similar genes for R3HDM1 using alignment to 12 protein entries: R3HD1_HUMAN (see all proteins):R3HDM ARPP21 R3HDM2
R3HDM1 for paralogs About GeneDecksing
|
Genomic Variants
for R3HDM1 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, 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
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 2 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for R3HDM1 (136289025 - 136482840 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for R3HDM1
1 CNV: 47933 | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing R3HDM1 |
|
Disorders
/ Diseases
for R3HDM1 gene
(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.)
About This Section
|
R3HDM1 for disorders About GeneDecksing
1  disease for R3HDM1: About MalaCardsataxia
Human Genome Epidemiology (HuGE) Navigator: R3HDM1 (2 documents)
Export disorders for R3HDM1 gene to outside databases
|
Publications
for R3HDM1 gene (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 R3HDM1 gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with R3HDM1) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Prediction of the coding sequences of unidentified human genes. I. The coding sequences of 40 new genes (KIAA0001-KIAA0040) deduced by analysis of randomly sampled cDNA clones from human immature myeloid cell line KG-1. (PubMed id 7584026)1, 2, 3 Nomura N.... Tabata S. (1994)
- Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. (PubMed id 15144186)1, 2 Brill L.M....Peters E.C. (2004)
- 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)
- System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
- Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (2010)
- Coeliac disease associated risk variants in TNFAIP3 and REL implicate altered NF-{kappa}B signalling. (PubMed id 19240061)1 Trynka G....Wijmenga C. (2009)
- Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (2009)
- A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (2008)
- A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. (PubMed id 16713569)1 Lim J.... Zoghbi H.Y. (2006)
- Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites. (PubMed id 15570572)1 Ficarro S.B....Peters E.C. (2005)
|
External Searches for R3HDM1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing R3HDM1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing R3HDM1 gene
(According to HUGE)
About This Section
| |
Specialized Databases showing R3HDM1 gene(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
|
| Name | Description |
| PharmGKB entry for R3HDM1 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for R3HDM1 gene:
Search GeneIP for patents involving R3HDM1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for R3HDM1 gene(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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, 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
About This Section
|
 | |
 | |
 |
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 | | | R3HDM1 Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for R3HDM1 |
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| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat R3HDM1 |
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