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Aliases for R3HDM1 Gene

Aliases for R3HDM1 Gene

  • R3H Domain Containing 1 2 3 5
  • R3H Domain (Binds Single-Stranded Nucleic Acids) Containing 2 3
  • R3HDM 3 4
  • R3H Domain-Containing Protein 1 3
  • KIAA0029 4

External Ids for R3HDM1 Gene

Previous HGNC Symbols for R3HDM1 Gene

  • R3HDM

Previous GeneCards Identifiers for R3HDM1 Gene

  • GC02P136123
  • GC02P136005
  • GC02P136289
  • GC02P128281

Summaries for R3HDM1 Gene

GeneCards Summary for R3HDM1 Gene

R3HDM1 (R3H Domain Containing 1) is a Protein Coding gene. GO annotations related to this gene include nucleic acid binding and poly(A) RNA binding. An important paralog of this gene is R3HDM2.

Additional gene information for R3HDM1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for R3HDM1 Gene

Genomics for R3HDM1 Gene

Regulatory Elements for R3HDM1 Gene

Enhancers for R3HDM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02H136247 1.9 FANTOM5 Ensembl ENCODE dbSUPER 4.7 +716.7 716698 1 FEZF1 GLI4 ZNF2 GLIS2 FOS SP3 YY2 REST TSHZ1 ZNF488 UBXN4 SMC4P1 ZRANB3 R3HDM1 CXCR4 ENSG00000279024 UBBP1
GH02H136253 1.7 FANTOM5 Ensembl ENCODE dbSUPER 4.7 +723.5 723535 3 HDGF PKNOX1 ATF1 RB1 YBX1 BATF RAD21 ATF7 ETV6 RUNX3 CXCR4 R3HDM1 MCM6 DARS-AS1 ENSG00000279024 UBBP1
GH02H135556 0.3 FANTOM5 12.9 +25.3 25263 0 ZRANB3 R3HDM1 RAB3GAP1 MAP3K19 GC02M135657
GH02H135632 0.3 FANTOM5 10.3 +101.1 101092 0 RNU6-512P R3HDM1 ZRANB3 GC02M135657
GH02H135646 0.3 FANTOM5 1.6 +115.6 115625 0 R3HDM1 GC02M135657
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around R3HDM1 on UCSC Golden Path with GeneCards custom track

Genomic Location for R3HDM1 Gene

Chromosome:
2
Start:
135,531,455 bp from pter
End:
135,725,270 bp from pter
Size:
193,816 bases
Orientation:
Plus strand

Genomic View for R3HDM1 Gene

Genes around R3HDM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
R3HDM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for R3HDM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for R3HDM1 Gene

Proteins for R3HDM1 Gene

  • Protein details for R3HDM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15032-R3HD1_HUMAN
    Recommended name:
    R3H domain-containing protein 1
    Protein Accession:
    Q15032
    Secondary Accessions:
    • A8K1V0
    • B3KXQ9
    • E9PBB4
    • E9PG42
    • G5E9G8
    • Q8IW32

    Protein attributes for R3HDM1 Gene

    Size:
    1099 amino acids
    Molecular mass:
    120696 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA04878.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for R3HDM1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for R3HDM1 Gene

Post-translational modifications for R3HDM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for R3HDM1 Gene

Domains & Families for R3HDM1 Gene

Gene Families for R3HDM1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for R3HDM1 Gene

Suggested Antigen Peptide Sequences for R3HDM1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with R3HDM1: view

No data available for UniProtKB/Swiss-Prot for R3HDM1 Gene

Function for R3HDM1 Gene

Gene Ontology (GO) - Molecular Function for R3HDM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
genes like me logo Genes that share ontologies with R3HDM1: view

Phenotypes for R3HDM1 Gene

genes like me logo Genes that share phenotypes with R3HDM1: view

Animal Models for R3HDM1 Gene

MGI Knock Outs for R3HDM1:

Animal Model Products

CRISPR Products

miRNA for R3HDM1 Gene

miRTarBase miRNAs that target R3HDM1

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for R3HDM1 Gene

Localization for R3HDM1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for R3HDM1 gene
Compartment Confidence
nucleus 4
cytosol 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for R3HDM1 Gene

Pathways & Interactions for R3HDM1 Gene

SuperPathways for R3HDM1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for R3HDM1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for R3HDM1 Gene

Drugs & Compounds for R3HDM1 Gene

No Compound Related Data Available

Transcripts for R3HDM1 Gene

Unigene Clusters for R3HDM1 Gene

R3H domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for R3HDM1 Gene

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:
SP6: - - - - - -
SP7: - -
SP8:
SP9:
SP10:
SP11: - -
SP12: - - -
SP13:
SP14: - - -
SP15: - - - -
SP16:
SP17: - - - - - -

ExUns: 17a · 17b ^ 18a · 18b ^ 19a · 19b · 19c ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28
SP1:
SP2: - -
SP3:
SP4:
SP5: - -
SP6:
SP7:
SP8:
SP9:
SP10: - -
SP11:
SP12:
SP13: -
SP14:
SP15:
SP16:
SP17:

Relevant External Links for R3HDM1 Gene

GeneLoc Exon Structure for
R3HDM1
ECgene alternative splicing isoforms for
R3HDM1

Expression for R3HDM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for R3HDM1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for R3HDM1 Gene

This gene is overexpressed in Brain - Cortex (x5.4), Brain - Frontal Cortex (BA9) (x5.3), and Brain - Anterior cingulate cortex (BA24) (x4.5).

Protein differential expression in normal tissues from HIPED for R3HDM1 Gene

This gene is overexpressed in Breast (49.8) and Stomach (16.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for R3HDM1 Gene



NURSA nuclear receptor signaling pathways regulating expression of R3HDM1 Gene:

R3HDM1

SOURCE GeneReport for Unigene cluster for R3HDM1 Gene:

Hs.412462

Evidence on tissue expression from TISSUES for R3HDM1 Gene

  • Nervous system(4.8)
  • Bone marrow(4.2)
genes like me logo Genes that share expression patterns with R3HDM1: view

Primer Products

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for R3HDM1 Gene

Orthologs for R3HDM1 Gene

This gene was present in the common ancestor of animals.

Orthologs for R3HDM1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia R3HDM1 33 34
  • 99.64 (n)
cow
(Bos Taurus)
Mammalia R3HDM1 33 34
  • 94.34 (n)
dog
(Canis familiaris)
Mammalia R3HDM1 33 34
  • 94.12 (n)
mouse
(Mus musculus)
Mammalia R3hdm1 33 16 34
  • 90.04 (n)
rat
(Rattus norvegicus)
Mammalia R3hdm1 33
  • 89.02 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia R3HDM1 34
  • 82 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia R3HDM1 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves R3HDM1 33 34
  • 80.96 (n)
lizard
(Anolis carolinensis)
Reptilia R3HDM1 34
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia r3hdm1 33
  • 71.95 (n)
zebrafish
(Danio rerio)
Actinopterygii r3hdm1 33 34
  • 62.56 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta enc 34
  • 11 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea ZK121.2 34
  • 25 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 19 (a)
OneToMany
Species where no ortholog for R3HDM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for R3HDM1 Gene

ENSEMBL:
Gene Tree for R3HDM1 (if available)
TreeFam:
Gene Tree for R3HDM1 (if available)

Paralogs for R3HDM1 Gene

Paralogs for R3HDM1 Gene

genes like me logo Genes that share paralogs with R3HDM1: view

Variants for R3HDM1 Gene

Sequence variations from dbSNP and Humsavar for R3HDM1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000005411 -- 135,560,066(+) TGATG(G/T)CATGG intron-variant
rs1000021051 -- 135,599,404(+) ATACT(C/T)GAATG intron-variant
rs1000036369 -- 135,687,230(+) GTAGA(A/G)GCAGA intron-variant
rs1000049869 -- 135,708,626(+) CTTCA(G/T)AGATA intron-variant
rs1000084784 -- 135,531,611(+) AACCG(-/CCT)CCTCC nc-transcript-variant, upstream-variant-2KB, cds-indel

Structural Variations from Database of Genomic Variants (DGV) for R3HDM1 Gene

Variant ID Type Subtype PubMed ID
esv2720864 CNV deletion 23290073
esv34026 CNV loss 18971310
esv3560188 CNV deletion 23714750
nsv1000750 CNV gain 25217958
nsv1120382 CNV tandem duplication 24896259
nsv1136419 CNV deletion 24896259

Variation tolerance for R3HDM1 Gene

Residual Variation Intolerance Score: 15.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.94; 94.91% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for R3HDM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
R3HDM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for R3HDM1 Gene

Disorders for R3HDM1 Gene

Relevant External Links for R3HDM1

Genetic Association Database (GAD)
R3HDM1
Human Genome Epidemiology (HuGE) Navigator
R3HDM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
R3HDM1

No disorders were found for R3HDM1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for R3HDM1 Gene

Publications for R3HDM1 Gene

  1. 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. (PMID: 7584026) Nomura N … Tabata S (DNA research : an international journal for rapid publication of reports on genes and genomes 1994) 2 3 4 60
  2. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 45 60
  3. Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. (PMID: 15144186) Brill LM … Peters EC (Analytical chemistry 2004) 3 4 60
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 60

Products for R3HDM1 Gene

Sources for R3HDM1 Gene

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