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
  • R3H Domain-Containing Protein 1 3 4
  • KIAA0029 2 4
  • R3HDM 3 4
  • R3HDM1 5

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. Diseases associated with R3HDM1 include Ichthyosis, Congenital, Autosomal Recessive 11 and Autosomal Recessive Congenital Ichthyosis. Gene Ontology (GO) annotations related to this gene include nucleic acid binding. An important paralog of this gene is R3HDM2.

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for R3HDM1 Gene

Genomics for R3HDM1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for R3HDM1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J135529 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 264.1 +0.1 77 5 CHD2 TBP MXD4 SP1 FEZF1 CEBPA SIX5 NR2C1 MNT BRCA1 R3HDM1 ZRANB3 CCNT2 UBXN4 MCM6 MAP3K19 lnc-UBXN4-11
GH02J135586 Promoter/Enhancer 0.8 EPDnew Ensembl 261.2 +54.6 54572 1.2 CTCF CEBPB POLR2A RAD21 R3HDM1 ZRANB3 MAP3K19 RAB3GAP1 RF00017-3319 HSALNG0019064 UBXN4
GH02J135741 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 13.6 +212.2 212173 5.2 CHD2 TBP MXD4 CEBPA SIX5 SMAD5 ETS1 IRF2 MBD2 ZNF217 UBXN4 LOC107985946 NONHSAG029369.2 CCNT2 R3HDM1 DARS1 MCM6 MAP3K19 NONHSAG029370.2 LCT
GH02J135664 Enhancer 0.7 Ensembl 10.8 +134.6 134572 3.6 SP1 BCL11A IRF4 EBF1 CBFB BATF MAFK NFATC1 IKZF1 TCF7 MIR128-1 R3HDM1 ZRANB3 RAB3GAP1 MAP3K19 DARS1 UBXN4 MCM6 NONHSAG029367.2 piR-61029-084
GH02J135004 Enhancer 0.7 Ensembl 9.4 -526.9 -526929 0.8 CTCF REST TRIM22 SMC3 RAD21 KLF9 TCF7L2 MBD1 MAX RB1 MAP3K19 RAB3GAP1 SNORA40B R3HDM1 ZRANB3 DARS1 MCM6 MK280269-038 piR-57337-024 HSALNG0019043
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around R3HDM1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for R3HDM1

Top Transcription factor binding sites by QIAGEN in the R3HDM1 gene promoter:
  • AML1a
  • AP-2alpha
  • AP-2alpha isoform 2
  • AP-2alpha isoform 3
  • AP-2alpha isoform 4
  • E47
  • p300
  • Tal-1
  • USF-1
  • USF1

Genomic Locations for R3HDM1 Gene

Latest Assembly
chr2:135,531,429-135,725,270
(GRCh38/hg38)
Size:
193,842 bases
Orientation:
Plus strand

Previous Assembly
chr2:136,289,054-136,482,839
(GRCh37/hg19 by Entrez Gene)
Size:
193,786 bases
Orientation:
Plus strand

chr2:136,289,025-136,482,840
(GRCh37/hg19 by Ensembl)
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=Extended N-terminus.; 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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for R3HDM1 Gene

InterPro:
Blocks:
  • Single-stranded nucleic acid binding R3H
ProtoNet:

Suggested Antigen Peptide Sequences for R3HDM1 Gene

GenScript: Design optimal peptide antigens:
  • R3HDM1 protein (Q9BVG5_HUMAN)
  • R3H domain-containing protein 1 (R3HD1_HUMAN)
genes like me logo Genes that share domains with R3HDM1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for R3HDM1 Gene

Function for R3HDM1 Gene

Phenotypes From GWAS Catalog for R3HDM1 Gene

Gene Ontology (GO) - Molecular Function for R3HDM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI --
genes like me logo Genes that share ontologies with R3HDM1: view
genes like me logo Genes that share phenotypes with R3HDM1: view

Animal Models for R3HDM1 Gene

MGI Knock Outs for R3HDM1:
  • R3hdm1 R3hdm1<tm1b(EUCOMM)Wtsi>

miRNA for R3HDM1 Gene

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for R3HDM1

No data available for Molecular function , Enzyme Numbers (IUBMB) , 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
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

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

PathCards logo

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

mRNA/cDNA for R3HDM1 Gene

7 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
20 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for R3HDM1

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

Expression for R3HDM1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for R3HDM1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for R3HDM1

SOURCE GeneReport for Unigene cluster for R3HDM1 Gene:

Hs.412462

Evidence on tissue expression from TISSUES for R3HDM1 Gene

  • Nervous system(4.9)
  • Bone marrow(4.2)
  • Muscle(2.2)
genes like me logo Genes that share expression patterns with R3HDM1: view

Primer products for research

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 30 31
  • 99.64 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia R3HDM1 30 31
  • 94.34 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia R3HDM1 30 31
  • 94.12 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia R3hdm1 30 17 31
  • 90.04 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia R3hdm1 30
  • 89.02 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia R3HDM1 31
  • 82 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia R3HDM1 31
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves R3HDM1 30 31
  • 80.96 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia R3HDM1 31
  • 77 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia r3hdm1 30
  • 71.95 (n)
Zebrafish
(Danio rerio)
Actinopterygii r3hdm1 30 31
  • 62.56 (n)
OneToOne
-- 30
Fruit Fly
(Drosophila melanogaster)
Insecta enc 31
  • 11 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ZK121.2 31
  • 25 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 19 (a)
OneToMany
Species where no ortholog for R3HDM1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for R3HDM1: view image

Paralogs for R3HDM1 Gene

Paralogs for R3HDM1 Gene

(3) SIMAP similar genes for R3HDM1 Gene using alignment to 12 proteins:

  • R3HD1_HUMAN
  • C9JIX1_HUMAN
  • C9JIX3_HUMAN
  • E9PBB4_HUMAN
  • E9PG42_HUMAN
  • G5E9G8_HUMAN
  • H7BZ47_HUMAN
  • H7C1X4_HUMAN
  • H7C207_HUMAN
  • H7C2F9_HUMAN
  • H7C3T7_HUMAN
  • Q9BVG5_HUMAN
genes like me logo Genes that share paralogs with R3HDM1: view

Variants for R3HDM1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for R3HDM1 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs2305165 - p.Gln632Pro
rs961360 - p.Met270Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for R3HDM1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for R3HDM1 Gene

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

SNP Genotyping and Copy Number Assays for research

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

Disorders for R3HDM1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for R3HDM1 Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for R3HDM1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with R3HDM1: view

No data available for 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
  2. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. (PMID: 19240061) Trynka G … Wijmenga C (Gut 2009) 3 41
  3. 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
  4. 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
  5. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. (PMID: 33060197) Gordon DE … Krogan NJ (Science (New York, N.Y.) 2020) 3

Products for R3HDM1 Gene

Sources for R3HDM1 Gene