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R3HDM1 R3H domain containing 1 [ Homo sapiens (human) ]

Gene ID: 23518, updated on 27-Nov-2024

Summary

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Official Symbol
R3HDM1provided by HGNC
Official Full Name
R3H domain containing 1provided by HGNC
Primary source
HGNC:HGNC:9757
See related
Ensembl:ENSG00000048991 MIM:619474; AllianceGenome:HGNC:9757
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
R3HDM
Summary
Enables RNA binding activity. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in brain (RPKM 20.1), testis (RPKM 10.5) and 23 other tissues See more
Orthologs
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Genomic context

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See R3HDM1 in Genome Data Viewer
Location:
2q21.3
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (135531484..135725269)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (135972007..136165780)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (136289054..136482839)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906077 Neighboring gene zinc finger RANBP2-type containing 3 Neighboring gene MPRA-validated peak3875 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16571 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16572 Neighboring gene Sharpr-MPRA regulatory region 5980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11981 Neighboring gene G3BP1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16574 Neighboring gene uncharacterized LOC124907893 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16575 Neighboring gene RNA, U6 small nuclear 512, pseudogene Neighboring gene microRNA 128-1 Neighboring gene uncharacterized LOC107985946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16577 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:136499891-136500666 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:136554979-136555500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:136555501-136556024 Neighboring gene UBX domain protein 4 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:136574960-136576159 Neighboring gene LCT antisense RNA 1 Neighboring gene lactase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. R3HDM1 haploinsufficiency is associated with mild intellectual disability. Fukushi D, et al. Am J Med Genet A, 2021 Jun. PMID 33750005
  2. Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites. Ficarro SB, et al. Rapid Commun Mass Spectrom, 2005. PMID 15570572
  3. 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). Nomura N, et al. DNA Res, 1994. PMID 7584028
  4. 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. Nomura N, et al. DNA Res, 1994. PMID 7584026
  5. Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. Brill LM, et al. Anal Chem, 2004 May 15. PMID 15144186

See all (48) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. R3HDM1 haploinsufficiency is associated with mild intellectual disability.
    Title: R3HDM1 haploinsufficiency is associated with mild intellectual disability.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of R3H domain containing 1 (R3HDM1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ23334, KIAA0029

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
R3H domain-containing protein 1
Names
R3H domain (binds single-stranded nucleic acids) containing

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001282798.2 → NP_001269727.1  R3H domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_001269727.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AC011893, AC016742, AK290015, BQ011745, D21852, DA324823
    Consensus CDS
    CCDS63025.1
    UniProtKB/Swiss-Prot
    Q15032
    Related
    ENSP00000387010.1, ENST00000409606.5
    Conserved Domains (3) summary
    cd02642
    Location:167 → 228
    R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
    pfam09606
    Location:579 → 910
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam12752
    Location:251 → 302
    SUZ; SUZ domain

  2. NM_001282799.2 → NP_001269728.1  R3H domain-containing protein 1 isoform c

    See identical proteins and their annotated locations for NP_001269728.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks two alternate exons that result in the loss of an in-frame segment in the 5' coding region, and lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
    Source sequence(s)
    AC016742, AL704414, BQ011745, D21852
    Consensus CDS
    CCDS63026.1
    UniProtKB/TrEMBL
    B4DLH6
    Related
    ENSP00000386457.1, ENST00000409478.5
    Conserved Domains (2) summary
    cd02642
    Location:123 → 184
    R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
    pfam12752
    Location:205 → 258
    SUZ; SUZ domain

  3. NM_001282800.2 → NP_001269729.1  R3H domain-containing protein 1 isoform d

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks three alternate exons in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (d) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AC016742, AK127793, BQ011745
    Consensus CDS
    CCDS63024.1
    UniProtKB/Swiss-Prot
    Q15032
    Related
    ENSP00000386877.1, ENST00000410054.5
    Conserved Domains (2) summary
    cd02642
    Location:111 → 172
    R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
    pfam12752
    Location:193 → 246
    SUZ; SUZ domain

  4. NM_001354199.2 → NP_001341128.1  R3H domain-containing protein 1 isoform b

    Status: VALIDATED

    Source sequence(s)
    AC011893, AC016742, BQ011745
    Consensus CDS
    CCDS2177.1
    UniProtKB/Swiss-Prot
    A8K1V0, B3KXQ9, E9PBB4, E9PG42, G5E9G8, Q15032, Q8IW32
    Conserved Domains (3) summary
    cd02642
    Location:167 → 228
    R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
    pfam09606
    Location:578 → 909
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam12752
    Location:251 → 302
    SUZ; SUZ domain

  5. NM_001354200.2 → NP_001341129.1  R3H domain-containing protein 1 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Both variants 1 and 6 encoded the same isoform (a).
    Source sequence(s)
    AC011893, AC016742, BQ011745
    Consensus CDS
    CCDS63025.1
    Conserved Domains (3) summary
    cd02642
    Location:167 → 228
    R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
    pfam09606
    Location:579 → 910
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam12752
    Location:251 → 302
    SUZ; SUZ domain

  6. NM_001378107.1 → NP_001365036.1  R3H domain-containing protein 1 isoform e

    Status: VALIDATED

    Source sequence(s)
    AC011893, AC016742
    Consensus CDS
    CCDS92870.1
    UniProtKB/TrEMBL
    A0A804HIA8
    Related
    ENSP00000506980.1, ENST00000683871.1
    Conserved Domains (3) summary
    cd02642
    Location:167 → 228
    R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
    pfam03157
    Location:653 → 855
    Glutenin_hmw; High molecular weight glutenin subunit
    pfam12752
    Location:251 → 302
    SUZ; SUZ domain

  7. NM_015361.4 → NP_056176.2  R3H domain-containing protein 1 isoform b

    See identical proteins and their annotated locations for NP_056176.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, and uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (b) is 1 aa shorter than isoform a.
    Source sequence(s)
    AK026987, AL704414, BC041093, BQ011745
    Consensus CDS
    CCDS2177.1
    UniProtKB/Swiss-Prot
    A8K1V0, B3KXQ9, E9PBB4, E9PG42, G5E9G8, Q15032, Q8IW32
    Related
    ENSP00000264160.4, ENST00000264160.8
    Conserved Domains (3) summary
    cd02642
    Location:167 → 228
    R3H_encore_like; R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H ...
    pfam09606
    Location:578 → 909
    Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
    pfam12752
    Location:251 → 302
    SUZ; SUZ domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    135531484..135725269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    135972007..136165780
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15032.3 GenPept UniProtKB/Swiss-Prot:Q15032

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