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Aliases for RGPD3 Gene

Aliases for RGPD3 Gene

  • RANBP2-Like And GRIP Domain Containing 3 2 3 5
  • RGP3 3 4
  • RanBP2-Like And GRIP Domain-Containing Protein 3 3

External Ids for RGPD3 Gene

Previous GeneCards Identifiers for RGPD3 Gene

  • GC00U921699
  • GC02U900831
  • GC02M107007

Summaries for RGPD3 Gene

Entrez Gene Summary for RGPD3 Gene

  • This gene is located in a cluster of Ran-binding protein related genes on chromosome 2 which arose through duplication in primates. The encoded protein contains an N-terminal TPR (tetratricopeptide repeat) domain, two Ran-binding domains, and a C-terminal GRIP domain (golgin-97, RanBP2alpha, Imh1p and p230/golgin-245) domain. [provided by RefSeq, Sep 2011]

GeneCards Summary for RGPD3 Gene

RGPD3 (RANBP2-Like And GRIP Domain Containing 3) is a Protein Coding gene. Among its related pathways are RNA transport. An important paralog of this gene is RGPD4.

Additional gene information for RGPD3 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RGPD3 Gene

Genomics for RGPD3 Gene

GeneHancer (GH) Regulatory Elements for RGPD3 Gene

Promoters and enhancers for RGPD3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I106468 Promoter 0.5 EPDnew 550.8 -0.1 -57 0.1 LOC105373534 RGPD3 ENSG00000237666
GH02I106465 Promoter 0.5 Ensembl 0.8 +2.5 2475 1.4 PIR53966 RGPD3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RGPD3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RGPD3 gene promoter:

Genomic Locations for RGPD3 Gene

Genomic Locations for RGPD3 Gene
77,087 bases
Minus strand

Genomic View for RGPD3 Gene

Genes around RGPD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RGPD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RGPD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RGPD3 Gene

Proteins for RGPD3 Gene

  • Protein details for RGPD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    RanBP2-like and GRIP domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • B8ZZM4

    Protein attributes for RGPD3 Gene

    1758 amino acids
    Molecular mass:
    197487 Da
    Quaternary structure:
    No Data Available
    • One of the 8 copies of RANBP2 clustered close to the chromosome 2 centromere.

neXtProt entry for RGPD3 Gene

Post-translational modifications for RGPD3 Gene

No Post-translational modifications

Other Protein References for RGPD3 Gene

No data available for DME Specific Peptides for RGPD3 Gene

Domains & Families for RGPD3 Gene

Gene Families for RGPD3 Gene

Suggested Antigen Peptide Sequences for RGPD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RGPD3: view

No data available for UniProtKB/Swiss-Prot for RGPD3 Gene

Function for RGPD3 Gene

Animal Model Products

CRISPR Products

miRNA for RGPD3 Gene

miRTarBase miRNAs that target RGPD3

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RGPD3 Gene

Localization for RGPD3 Gene

Subcellular locations from

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 RGPD3 gene
Compartment Confidence
cytosol 3
nucleus 2
plasma membrane 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear membrane (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RGPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
genes like me logo Genes that share ontologies with RGPD3: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for RGPD3 Gene

Pathways & Interactions for RGPD3 Gene

SuperPathways for RGPD3 Gene

SuperPathway Contained pathways
1 RNA transport
genes like me logo Genes that share pathways with RGPD3: view

Pathways by source for RGPD3 Gene

1 KEGG pathway for RGPD3 Gene

Gene Ontology (GO) - Biological Process for RGPD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046907 intracellular transport IEA --
genes like me logo Genes that share ontologies with RGPD3: view

No data available for SIGNOR curated interactions for RGPD3 Gene

Drugs & Compounds for RGPD3 Gene

No Compound Related Data Available

Transcripts for RGPD3 Gene

mRNA/cDNA for RGPD3 Gene

(4) REFSEQ mRNAs :
(1) Additional mRNA sequences :
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RGPD3 Gene

RANBP2-like and GRIP domain containing 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RGPD3 Gene

No ASD Table

Relevant External Links for RGPD3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RGPD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RGPD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RGPD3 Gene

This gene is overexpressed in Testis (x13.1).

Protein differential expression in normal tissues from HIPED for RGPD3 Gene

This gene is overexpressed in Pancreas (23.2), Serum (14.8), Brain (14.1), and Heart (12.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RGPD3 Gene

Protein tissue co-expression partners for RGPD3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RGPD3 Gene:


SOURCE GeneReport for Unigene cluster for RGPD3 Gene:

genes like me logo Genes that share expression patterns with RGPD3: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RGPD3 Gene

Orthologs for RGPD3 Gene

This gene was present in the common ancestor of animals.

Orthologs for RGPD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia -- 34
  • 96 (a)
-- 34
  • 96 (a)
-- 34
  • 90 (a)
-- 34
  • 81 (a)
(Mus musculus)
Mammalia Ranbp2 33
  • 87.97 (n)
(Bos Taurus)
Mammalia RANBP2 33
  • 85.32 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 82 (a)
-- 34
  • 76 (a)
(Gallus gallus)
Aves RANBP2 33
  • 71 (n)
-- 34
  • 60 (a)
-- 34
  • 48 (a)
-- 34
  • 44 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 42 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ranbp2 33
  • 66.56 (n)
(Danio rerio)
Actinopterygii si:ch1073-55a19.2 33
  • 56.38 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5071 34
  • 14 (a)
(Caenorhabditis elegans)
Secernentea Y17G9B.4 34
  • 13 (a)
T22F3.12 34
  • 7 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 4 (a)
Species where no ortholog for RGPD3 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)
  • dog (Canis familiaris)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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 RGPD3 Gene

Gene Tree for RGPD3 (if available)
Gene Tree for RGPD3 (if available)

Paralogs for RGPD3 Gene

(8) SIMAP similar genes for RGPD3 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with RGPD3: view

Variants for RGPD3 Gene

Sequence variations from dbSNP and Humsavar for RGPD3 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000067887 -- 106,437,531(-) AAAA/AAA intron_variant
rs1000135126 -- 106,449,620(-) G/A intron_variant
rs1000165143 -- 106,404,492(-) T/C downstream_transcript_variant
rs1000176027 -- 106,414,266(-) G/T genic_downstream_transcript_variant, intron_variant
rs1000285554 -- 106,413,697(-) G/A genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RGPD3 Gene

Variant ID Type Subtype PubMed ID
nsv961991 CNV duplication 23825009
nsv961471 CNV duplication 23825009
nsv953782 CNV duplication 24416366
nsv834322 CNV gain 17160897
nsv1146327 CNV duplication 26484159
esv3591872 CNV gain 21293372
esv3591871 CNV loss 21293372
esv3591865 CNV loss 21293372
esv29426 CNV gain+loss 19812545
esv2720482 CNV deletion 23290073
esv1179092 CNV insertion 17803354
dgv6988n54 CNV loss 21841781
dgv4034n100 CNV gain 25217958

Variation tolerance for RGPD3 Gene

Residual Variation Intolerance Score: 99% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.87; 91.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RGPD3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RGPD3 Gene

Disorders for RGPD3 Gene

Additional Disease Information for RGPD3

No disorders were found for RGPD3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RGPD3 Gene

Publications for RGPD3 Gene

  1. Complex genomic rearrangements lead to novel primate gene function. (PMID: 15710750) Ciccarelli FD … Bork P (Genome research 2005) 2 3 4 58
  2. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 2 3 4 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. Interactions of the Antiviral Factor Interferon Gamma-Inducible Protein 16 (IFI16) Mediate Immune Signaling and Herpes Simplex Virus-1 Immunosuppression. (PMID: 25693804) Diner BA … Cristea IM (Molecular & cellular proteomics : MCP 2015) 3 58
  5. Quantitative Proteomics Reveals Dynamic Interactions of the Minichromosome Maintenance Complex (MCM) in the Cellular Response to Etoposide Induced DNA Damage. (PMID: 25963833) Drissi R … Boisvert FM (Molecular & cellular proteomics : MCP 2015) 3 58

Products for RGPD3 Gene

Sources for RGPD3 Gene

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