Human Gene R3HDM1 (uc002tuo.3)
  Description: Homo sapiens R3H domain containing 1 (R3HDM1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr2:136,289,083-136,482,839 Size: 193,757 Total Exon Count: 26 Strand: +
Coding Region
   Position: hg19 chr2:136,362,416-136,481,862 Size: 119,447 Coding Exon Count: 24 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:136,289,083-136,482,839)mRNA (may differ from genome)Protein (1099 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: R3HD1_HUMAN
DESCRIPTION: RecName: Full=R3H domain-containing protein 1;
SIMILARITY: Contains 1 R3H domain.
SIMILARITY: Contains 1 SUZ domain.
SEQUENCE CAUTION: Sequence=BAA04878.2; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): R3HDM1
CDC HuGE Published Literature: R3HDM1
Positive Disease Associations: Neuroblastoma , Triglycerides
Related Studies:
  1. Neuroblastoma
    John M Maris et al. The New England journal of medicine 2008, Chromosome 6p22 locus associated with clinically aggressive neuroblastoma., The New England journal of medicine. [PubMed 18463370]
    A common genetic variation at chromosome band 6p22 is associated with susceptibility to neuroblastoma.
  2. Neuroblastoma
    John M Maris et al. The New England journal of medicine 2008, Chromosome 6p22 locus associated with clinically aggressive neuroblastoma., The New England journal of medicine. [PubMed 18463370]
    A common genetic variation at chromosome band 6p22 is associated with susceptibility to neuroblastoma.
  3. Triglycerides
    , , . [PubMed 0]
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 35.91 RPKM in Brain - Cortex
Total median expression: 385.65 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -107.00370-0.289 Picture PostScript Text
3' UTR -235.50977-0.241 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001374 - R3H_ss-bd
IPR024771 - SUZ

Pfam Domains:
PF01424 - R3H domain
PF12752 - SUZ domain

SCOP Domains:
82708 - R3H domain

ModBase Predicted Comparative 3D Structure on Q15032
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding


-  Descriptions from all associated GenBank mRNAs
  KJ904695 - Synthetic construct Homo sapiens clone ccsbBroadEn_14089 R3HDM1 gene, encodes complete protein.
BC001217 - Homo sapiens R3H domain containing 1, mRNA (cDNA clone IMAGE:3356812), complete cds.
D21852 - Homo sapiens KIAA0029 mRNA.
BC041093 - Homo sapiens R3H domain containing 1, mRNA (cDNA clone MGC:46099 IMAGE:5556247), complete cds.
LF383640 - JP 2014500723-A/191143: Polycomb-Associated Non-Coding RNAs.
MA619217 - JP 2018138019-A/191143: Polycomb-Associated Non-Coding RNAs.
AK127793 - Homo sapiens cDNA FLJ45894 fis, clone OCBBF3023913, highly similar to R3H domain-containing protein 1.
AK290015 - Homo sapiens cDNA FLJ77529 complete cds, highly similar to Homo sapiens R3H domain containing 1 (R3HDM1), mRNA.
AB385267 - Synthetic construct DNA, clone: pF1KA0029, Homo sapiens R3HDM1 gene for R3H domain-containing protein 1, complete cds, without stop codon, in Flexi system.
AK297000 - Homo sapiens cDNA FLJ58151 complete cds, moderately similar to R3H domain-containing protein 1.
AK026987 - Homo sapiens cDNA: FLJ23334 fis, clone HEP12815.
JD389876 - Sequence 370900 from Patent EP1572962.
JD395311 - Sequence 376335 from Patent EP1572962.
JD277037 - Sequence 258061 from Patent EP1572962.
JD156907 - Sequence 137931 from Patent EP1572962.
JD279511 - Sequence 260535 from Patent EP1572962.
JD101210 - Sequence 82234 from Patent EP1572962.
LF319402 - JP 2014500723-A/126905: Polycomb-Associated Non-Coding RNAs.
LF319403 - JP 2014500723-A/126906: Polycomb-Associated Non-Coding RNAs.
LF319412 - JP 2014500723-A/126915: Polycomb-Associated Non-Coding RNAs.
LF319421 - JP 2014500723-A/126924: Polycomb-Associated Non-Coding RNAs.
MA554979 - JP 2018138019-A/126905: Polycomb-Associated Non-Coding RNAs.
MA554980 - JP 2018138019-A/126906: Polycomb-Associated Non-Coding RNAs.
MA554989 - JP 2018138019-A/126915: Polycomb-Associated Non-Coding RNAs.
MA554998 - JP 2018138019-A/126924: Polycomb-Associated Non-Coding RNAs.
LF319428 - JP 2014500723-A/126931: Polycomb-Associated Non-Coding RNAs.
JD378673 - Sequence 359697 from Patent EP1572962.
JD091606 - Sequence 72630 from Patent EP1572962.
JD292476 - Sequence 273500 from Patent EP1572962.
LF319429 - JP 2014500723-A/126932: Polycomb-Associated Non-Coding RNAs.
JD236512 - Sequence 217536 from Patent EP1572962.
LF319430 - JP 2014500723-A/126933: Polycomb-Associated Non-Coding RNAs.
JD492153 - Sequence 473177 from Patent EP1572962.
JD246395 - Sequence 227419 from Patent EP1572962.
JD168323 - Sequence 149347 from Patent EP1572962.
JD288670 - Sequence 269694 from Patent EP1572962.
JD020916 - Sequence 1940 from Patent EP1572962.
JD029262 - Sequence 10286 from Patent EP1572962.
MA555005 - JP 2018138019-A/126931: Polycomb-Associated Non-Coding RNAs.
MA555006 - JP 2018138019-A/126932: Polycomb-Associated Non-Coding RNAs.
MA555007 - JP 2018138019-A/126933: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA0029, NM_015361, NP_056176, Q15032, Q8IW32, R3HD1_HUMAN, R3HDM
UCSC ID: uc002tuo.3
RefSeq Accession: NM_015361
Protein: Q15032 (aka R3HD1_HUMAN)
CCDS: CCDS2177.1, CCDS63025.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015361.2
exon count: 26CDS single in 3' UTR: no RNA size: 4666
ORF size: 3300CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 6202.00frame shift in genome: no % Coverage: 99.59
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.