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R3HDM1 Gene

protein-coding GIFtS: 50

GC02P136005

R3H domain containing 1
(Previous name: R3H domain (binds single-stranded nucleic acids) containing )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: R3HDM)

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
About This Section

Aliases
FLJ23334 ^²
KIAA0029 ^¹, ², ³
R3HDM ^², ³

Descriptions
R3H domain (binds single-stranded nucleic acids) containing ^¹, ²
R3H domain containing 1 ^²

External Ids
HGNC: 9757¹
Entrez Gene: 23518²
UniProtKB: Q15032³
Ensembl: ENSG00000048991⁷

Search outside databases for aliases for R3HDM1 gene

Previous GC identifer: GC02P136123

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

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the R3HDM1 gene

Entrez Gene cytogenetic band: 2q21.3 Ensembl cytogenetic band: 2q21.3 HGNC cytogenetic band: 2p14-q21.3

R3HDM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 2 GeneLoc Exon Structure

GeneLoc location for GC02P136005: (about GC identifiers)

Start:	136,005,541 bp from pter
End:	136,199,309 bp from pter
Size:	193,769 bases
Orientation:	plus strand

RefSeq DNA sequence:

NC_000002.10 NT_022135.15

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: R3HD1_HUMAN, Q15032 (See protein sequence)

Recommended Name: R3H domain-containing protein 1

Size: 1099 amino acids; 120696 Da

Secondary accessions: Q8IW32

Alternative splicing: 2 isoforms: Q15032-1 Q15032-2

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_056176.2

ENSEMBL proteins:

ENSP00000386877 ENSP00000264160 ENSP00000331396 ENSP00000386457 ENSP00000387010

Human Recombinant Proteins

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	Browse Abnova for Human Recombinant Proteins

Browse Origene for full length recombinant human proteins expressed in human HEK293 cells

Antibodies for R3HDM1:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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	Browse Abnova for Monoclonal and Polyclonal Antibodies
	Search Novus for antibodies for R3HDM1

Assays for R3HDM1:

	Browse Invitrogen for biochemical assays
	Browse Kits and Assays available from Millipore
	Browse R&D Systems for biochemical assays
	Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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Graphical View of Domain Structure for InterPro Entry Q15032

ProtoNet protein and cluster: Q15032

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

UniProtKB/Swiss-Prot: R3HD1_HUMAN, Q15032

Similarity: Contains 1 R3H domain

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (R3HDM1)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (R3HDM1)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_015361

Applied Biosystems Silencer® siRNAs for R3HDM1

Sigma-Aldrich siRNA for R3HDM1

Sigma-Aldrich shRNA for R3HDM1

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for R3HDM1
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_015361
Myc/DDK tagged cDNA clone in CMV expression vector: NM_015361
untagged cDNA clone in CMV expression vector: NM_015361

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_015361

1 Gene Ontology (GO) molecular function term (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003676	nucleic acid binding	IEA	--

About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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1 Interacting protein for R3HDM1 (Q15032²) via UniProtKB, MINT, and/or STRING
Interactant Interaction Details
GeneCard External ID(s)
ATXN1 P54253² MINT-2871037
About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for R3HDM1

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (R3HDM1)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (R3HDM1)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_015361

Sigma-Aldrich siRNA for R3HDM1

Sigma-Aldrich shRNA for R3HDM1

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_015361

REFSEQ mRNAs for R3HDM1 gene:

NM_015361.2

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_015361

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_015361
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_015361
                                 untagged cDNA clone in CMV expression vector: NM_015361

Additional cDNA sequence:

AK026987.1 AK127793.1 AK290015.1 AK297000.1 BC001217.1 BC041093.1 D21852.1

20 DOTS entries:

DT.99936451 DT.444093 DT.97842133 DT.91765962 DT.91765965 DT.120981929 DT.120981938 DT.91734989

DT.91765960 DT.99994573 DT.100023489 DT.100783632 DT.120981932 DT.120981978 DT.120982014 DT.91937103

DT.92434780 DT.95275633 DT.99959947 DT.91765963

24/189 AceView cDNA sequences (see all 189 ):

AI276531 AA948164 BQ219803 AW188798 BX477821 AI802737 BM142469 CK820226

BG502255 D21852 AI074503 F09566 BM263173 BU521244 AW086199 BX472160

AA372108 AA514884 BE856664 AI420384 CD557193 BQ011745 F09539 AI983468

highest scoring ESTs for R3HDM1:

D21852 AA100742 AA214740 AA471019 AA504206 AA514884 AA832377 AA948164 AI004010 AI138870

Unigene Cluster for R3HDM1:

R3H domain containing 1

Hs.412462 [show with all ESTs]

Unigene Representative Sequence: NM_015361

GeneLoc Exon Structure

5/17 Alternative Splicing Database (ASD) splice patterns (SP) for R3HDM1 (see all 17 )

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	^
SP1:
SP2:
SP3:							-		-		-		-												-		-		-		-		-
SP4:																									-		-
SP5:

ExUns:	17a	·	17b	^	18a	·	18b	^	19a	·	19b	·	19c	^	20	^	21	^	22	^	23	^	24	^	25	^	26	^	27	^	28
SP1:
SP2:					-		-
SP3:
SP4:
SP5:					-		-

About this scheme

ECgene alternative splicing isoforms for R3HDM1

5 Ensembl transcripts including schematic representations:

ENST00000410054 ENST00000264160 ENST00000329971 ENST00000409478 ENST00000409606

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

R3HDM1 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for R3HDM1

¹ / ² / ³

5 probe-sets matching R3HDM1 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
36610_at²^{, 3}	U95-A	1	1.00	1.00	1.00	1.00	D21852	1.00	0.90	0.95	1
210714_at²^{, 3}	U133-A	1	1.00	1.00	--	--	BC001217	0.60	1.00	0.82	1
202754_at²^{, 3}	U133-A	1	1.00	1.00	--	--	NM_015361	0.60	1.00	0.82	1
210714_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
202754_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--

GeneDecks R3HDM1 for binary patterns associated with the probe-sets selected above

About GeneDecksing

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Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.412462
Expression variation in blood from EXPOLDB for R3HDM1

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section

Orthologs for R3HDM1 gene from 5/9 species (see all 9 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	R3HDM1¹	--	R3H domain containing 1	94.75(n) 96.18(a)	476129 XM_843499.1 XP_848592.1
chimpanzee (Pan troglodytes)	R3HDM1¹	--	R3H domain containing 1	89.85(n) 88.82(a)	459631 XM_001154261.1 XP_001154261.1
cow (Bos taurus)	R3HDM1¹	--	R3H domain containing 1	93.79(n) 95.09(a)	533850 XM_613390.3 XP_613390.3
rat (Rattus norvegicus)	R3hdm1¹	--	R3H domain containing 1	89.23(n) 90.42(a)	304763 XM_573442.2 XP_573442.1
mouse (Mus musculus)	R3hdm1^{1, 5}	1⁵	R3H domain 1 (binds single-stranded nucleic acids)^{1, 5}	90.47(n)¹ 91.17(a)¹	226412¹ NM_181750.2¹ NP_861415.2¹ AA674488⁵ AK051765⁵ (see all 24)

About this table Species with no ortholog for R3HDM1

ENSEMBL Gene Tree for R3HDM1

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

Paralogs for R3HDM1 gene

R3HDM2² ARPP-21²

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/683 NCBI SNPs in R3HDM1 are shown (see all 683 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 186)

AB	SNP ID	Valid	Chr 2 pos	Sequence	Recs	AA Chg	Type	More	Recs	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--			--
	rs961360^1,2	A,C,F,H,O	136110128(-)	`TCTCAT/CCTACA`	1	V/M	mis¹		20	NS EA NA EU WA	2834
	rs2305165^1,2	C,F,H,O	136126044(-)	`ATCCCT/GGCTGC`	1	P/Q	mis¹ ese³		12	EA NA EU WA	2430
	rs3739027^1,2	C,F,H	136198650(-)	`GCTGTA/GCAATA`	1	--	ut3¹ ese³		13	EA NA EU WA	2548
	rs13425947^1,2	F,H	136119531(+)	`GCCCCA/TCCTCA`	1	P/P	syn¹		4	EU EA WA	416
	rs2289959^1,2	A,C,F,H,O	136140374(-)	`TGTCAA/GTAAAG`	1	--	int¹		9	EA NA EU WA	2124
	rs1446584^1,2	A,C,F,H,O	136136431(-)	`AAGACC/TGCAAC`	1	--	int¹		17	EU EA WA NA	1580
	rs1374330^1,2	A,C,F,H,O	136137378(-)	`TCTCTT/GTTTTG`	1	--	int¹ trp³		7	EU EA WA NA	560
	rs1446585^1,2	A,C,F,H,O	136123949(-)	`GAGGAC/TGAACA`	1	--	int¹		7	EU EA WA NA	560
	rs313518^1,2	A,C,F,H,O	136155560(+)	`taaagT/Cgtgag`	1	--	int¹		5	MN EU EA WA	600
	rs2028239^1,2	A,C,F,H,O	136179301(+)	`CTAATT/GGCATG`	1	--	int¹		12	MN EU EA WA NA	1160

About this table

HapMap Linkage Disequilibrium images for R3HDM1 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

Human Genome Epidemiology Navigator: R3HDM1 (1 document)

(Possibly Related Articles in Doctor's Guide)
About This Section

(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
About This Section

10 PubMed articles for R3HDM1 gene:

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)^{2, 3, 4} 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)^{3, 4} 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)^{3, 4} Gerhard D.S....Malek J. (2004)
Coeliac disease associated risk variants in TNFAIP3 and REL implicate altered NF-{kappa}B signalling. (PubMed id 19240061)³ Trynka G....Wijmenga C. (2009)
A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)⁴ Dephoure N.... Gygi S.P. (2008)
Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry. (PubMed id 17287340)⁴ Molina H.... Pandey A. (2007)
A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. (PubMed id 16713569)³ 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)³ Ficarro S.B....Peters E.C. (2005)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)³ Strausberg R.L....Marra M.A. (2002)
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 (supplement). (PubMed id 7584028)³ Nomura N....Tabata S. (1994)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
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, and/or H-InvDB)
About This Section

Entrez Gene: 23518	HGNC: 9757	AceView: R3HDM	Ensembl:ENSG00000048991	euGenes: HUgn23518
ECgene: R3HDM1	H-InvDB: R3HDM1

(According to HUGE)
About This Section

HUGE: KIAA0029

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Licensable Technologies for R3HDM1
(Available from WIS Yeda, Salk, Tufts)

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(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
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Products for R3HDM1:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for R3HDM1-related products

	Millipore Custom Antibody & Bulk Services
	Millipore Preclinical / Clinical Development Services
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	Predesigned and custom siRNAs for R3HDM1		Browse antibodies at Sigma-Aldrich
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R3HDM1 Gene

protein-coding GIFtS: 50

Aliases &
Descriptions
for R3HDM1

Summaries
for R3HDM1

Genomic Location
for R3HDM1

Proteins
for R3HDM1

Protein Domains/
Families
for R3HDM1

Gene Function
for R3HDM1

Pathways & Interactions
for R3HDM1

Drugs & Compounds
for R3HDM1

Transcripts
for R3HDM1

Expression
for R3HDM1

Orthologs
for R3HDM1

Paralogs
for R3HDM1

SNPs/Variants
for R3HDM1

Disorders & Mutations
for R3HDM1

Medical News
for R3HDM1

Publications
for R3HDM1

Search for R3HDM1

Genome Databases showing R3HDM1

Other Databases showing R3HDM1

Specialized Databases showing R3HDM1

Licensable Technologies
for R3HDM1

Services
for R3HDM1

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

R3HDM1 Gene

protein-coding GIFtS: 50

Aliases & Descriptionsfor R3HDM1

Summariesfor R3HDM1

Genomic Locationfor R3HDM1

Proteinsfor R3HDM1

Protein Domains/Familiesfor R3HDM1

Gene Functionfor R3HDM1

Pathways & Interactionsfor R3HDM1

Drugs & Compoundsfor R3HDM1

Transcriptsfor R3HDM1

Expression for R3HDM1

Orthologsfor R3HDM1

Paralogsfor R3HDM1

SNPs/Variantsfor R3HDM1

Disorders & Mutationsfor R3HDM1

Medical Newsfor R3HDM1

Publicationsfor R3HDM1

Search for R3HDM1

Genome Databases showing R3HDM1

Other Databases showing R3HDM1

Specialized Databases showing R3HDM1

Licensable Technologiesfor R3HDM1

Servicesfor R3HDM1

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for R3HDM1

Summaries
for R3HDM1

Genomic Location
for R3HDM1

Proteins
for R3HDM1

Protein Domains/
Families
for R3HDM1

Gene Function
for R3HDM1

Pathways & Interactions
for R3HDM1

Drugs & Compounds
for R3HDM1

Transcripts
for R3HDM1

Expression
for R3HDM1

Orthologs
for R3HDM1

Paralogs
for R3HDM1

SNPs/Variants
for R3HDM1

Disorders & Mutations
for R3HDM1

Medical News
for R3HDM1

Publications
for R3HDM1

Licensable Technologies
for R3HDM1

Services
for R3HDM1