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Aliases for RGPD4 Gene

Aliases for RGPD4 Gene

  • RANBP2-Like And GRIP Domain Containing 4 2 3 5
  • RGP4 3 4
  • RanBP2-Like And GRIP Domain-Containing Protein 4 3

External Ids for RGPD4 Gene

Previous GeneCards Identifiers for RGPD4 Gene

  • GC02U900817
  • GC02M087836
  • GC02P107810
  • GC02P109910
  • GC02P108443

Summaries for RGPD4 Gene

GeneCards Summary for RGPD4 Gene

RGPD4 (RANBP2-Like And GRIP Domain Containing 4) is a Protein Coding gene. Among its related pathways are RNA transport. An important paralog of this gene is RGPD3.

Additional gene information for RGPD4 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 RGPD4 Gene

Genomics for RGPD4 Gene

GeneHancer (GH) Regulatory Elements for RGPD4 Gene

Promoters and enhancers for RGPD4 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
GH02I107826 Promoter 0.5 EPDnew 550.8 0.0 -4 0.1 RGPD4 RGPD4-AS1 GC02P107779
GH02I108532 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 4.5 +708.7 708665 5.9 HDGF CLOCK FOXA2 ZFP64 ARID4B SIN3A DMAP1 YY1 POLR2B ZNF213 LIMS1 GCC2-AS1 GCC2 SULT1C4 RGPD4 GC02P108499 PIR40245
GH02I107829 Promoter 0.5 Ensembl 20.2 +3.1 3069 1.2 RGPD4 PIR37300 GC02P107779
GH02I108572 Enhancer 1.1 Ensembl ENCODE dbSUPER 4.1 +748.0 747970 5.4 HDGF PAX8 CEBPG RELA ZNF121 POLR2A ATF7 FOSL2 FOS IKZF2 GCC2 LIMS1-AS1 SULT1C4 RGPD4 LIMS1 PIR40245
GH02I108313 Enhancer 0.9 Ensembl ENCODE 4.9 +488.8 488799 3.6 SOX13 TFAP4 KLF1 SAP130 ARID4B FEZF1 ZNF7 TEAD3 SLC30A9 ZNF121 PIR51121 SULT1C2P2 SULT1C2 LINC01594 RGPD4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RGPD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RGPD4 gene promoter:

Genomic Locations for RGPD4 Gene

Genomic Locations for RGPD4 Gene
chr2:107,826,932-107,892,544
(GRCh38/hg38)
Size:
65,613 bases
Orientation:
Plus strand
chr2:108,443,388-108,509,000
(GRCh37/hg19)

Genomic View for RGPD4 Gene

Genes around RGPD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RGPD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RGPD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RGPD4 Gene

Proteins for RGPD4 Gene

  • Protein details for RGPD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z3J3-RGPD4_HUMAN
    Recommended name:
    RanBP2-like and GRIP domain-containing protein 4
    Protein Accession:
    Q7Z3J3
    Secondary Accessions:
    • B9A029

    Protein attributes for RGPD4 Gene

    Size:
    1758 amino acids
    Molecular mass:
    197289 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • One of the 8 copies of RANBP2 clustered close to the chromosome 2 centromere.

    Alternative splice isoforms for RGPD4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RGPD4 Gene

Post-translational modifications for RGPD4 Gene

No Post-translational modifications

Other Protein References for RGPD4 Gene

No data available for DME Specific Peptides for RGPD4 Gene

Domains & Families for RGPD4 Gene

Gene Families for RGPD4 Gene

Suggested Antigen Peptide Sequences for RGPD4 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RGPD4: view

No data available for UniProtKB/Swiss-Prot for RGPD4 Gene

Function for RGPD4 Gene

Gene Ontology (GO) - Molecular Function for RGPD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 contributes_to GTPase activator activity IBA --
GO:0008536 Ran GTPase binding IBA --
genes like me logo Genes that share ontologies with RGPD4: view

Phenotypes for RGPD4 Gene

genes like me logo Genes that share phenotypes with RGPD4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RGPD4 Gene

Localization for RGPD4 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 RGPD4 gene
Compartment Confidence
nucleus 4
cytoskeleton 3
cytosol 3
plasma membrane 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear membrane (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RGPD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA --
GO:0005737 cytoplasm IBA --
GO:0005813 centrosome IBA --
genes like me logo Genes that share ontologies with RGPD4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for RGPD4 Gene

Pathways & Interactions for RGPD4 Gene

SuperPathways for RGPD4 Gene

SuperPathway Contained pathways
1 RNA transport
genes like me logo Genes that share pathways with RGPD4: view

Pathways by source for RGPD4 Gene

1 KEGG pathway for RGPD4 Gene

Gene Ontology (GO) - Biological Process for RGPD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000082 G1/S transition of mitotic cell cycle IBA --
GO:0006405 RNA export from nucleus IBA --
GO:0006511 ubiquitin-dependent protein catabolic process IBA --
GO:0006606 protein import into nucleus IBA --
GO:0007051 spindle organization IBA --
genes like me logo Genes that share ontologies with RGPD4: view

No data available for SIGNOR curated interactions for RGPD4 Gene

Drugs & Compounds for RGPD4 Gene

No Compound Related Data Available

Transcripts for RGPD4 Gene

mRNA/cDNA for RGPD4 Gene

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

Unigene Clusters for RGPD4 Gene

RANBP2-like and GRIP domain containing 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RGPD4 Gene

No ASD Table

Relevant External Links for RGPD4 Gene

GeneLoc Exon Structure for
RGPD4
ECgene alternative splicing isoforms for
RGPD4

Expression for RGPD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RGPD4 Gene

mRNA differential expression in normal tissues according to GTEx for RGPD4 Gene

This gene is overexpressed in Testis (x26.6).

Protein differential expression in normal tissues from HIPED for RGPD4 Gene

This gene is overexpressed in Brain (37.1) and Heart (31.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RGPD4 Gene



Protein tissue co-expression partners for RGPD4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RGPD4 Gene:

RGPD4

SOURCE GeneReport for Unigene cluster for RGPD4 Gene:

Hs.449164

Evidence on tissue expression from TISSUES for RGPD4 Gene

  • Eye(4.6)
  • Nervous system(4)
  • Liver(3.3)
  • Lung(2.9)
  • Stomach(2.1)
  • Intestine(2)
genes like me logo Genes that share expression patterns with RGPD4: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RGPD4 Gene

Orthologs for RGPD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for RGPD4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia -- 34
  • 96 (a)
ManyToMany
-- 34
  • 96 (a)
ManyToMany
-- 34
  • 90 (a)
ManyToMany
-- 34
  • 82 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Ranbp2 33
  • 87.87 (n)
cow
(Bos Taurus)
Mammalia RANBP2 33
  • 85.26 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 82 (a)
ManyToMany
-- 34
  • 76 (a)
ManyToMany
chicken
(Gallus gallus)
Aves RANBP2 33
  • 71.02 (n)
-- 34
  • 60 (a)
ManyToMany
-- 34
  • 48 (a)
ManyToMany
-- 34
  • 44 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 42 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia ranbp2 33
  • 66.69 (n)
zebrafish
(Danio rerio)
Actinopterygii si:ch1073-55a19.2 33
  • 56.71 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5071 34
  • 14 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y17G9B.4 34
  • 13 (a)
ManyToMany
T22F3.12 34
  • 7 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 4 (a)
OneToMany
Species where no ortholog for RGPD4 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 RGPD4 Gene

ENSEMBL:
Gene Tree for RGPD4 (if available)
TreeFam:
Gene Tree for RGPD4 (if available)

Paralogs for RGPD4 Gene

(8) SIMAP similar genes for RGPD4 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with RGPD4: view

Variants for RGPD4 Gene

Sequence variations from dbSNP and Humsavar for RGPD4 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs832358 benign, not specified 107,871,445(+) A/G coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs1000017831 -- 107,836,132(+) G/A intron_variant
rs1000018256 -- 107,855,354(+) C/T intron_variant
rs1000149172 -- 107,845,544(+) G/C intron_variant
rs1000194393 -- 107,887,923(+) T/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RGPD4 Gene

Variant ID Type Subtype PubMed ID
dgv4034n100 CNV gain 25217958
dgv61n68 CNV gain 17160897
dgv6988n54 CNV loss 21841781
dgv724e199 CNV deletion 23128226
esv1116837 CNV insertion 17803354
esv1536919 CNV deletion 17803354
esv2475213 CNV loss 19546169
esv2720482 CNV deletion 23290073
esv2720498 CNV deletion 23290073
esv27269 CNV gain+loss 19812545
esv2759081 CNV gain 17122850
esv3591913 CNV gain 21293372
esv995182 CNV loss 20482838
nsv1118872 CNV deletion 24896259
nsv1126558 CNV deletion 24896259
nsv582636 CNV loss 21841781
nsv829610 CNV gain 20364138
nsv829611 CNV gain 20364138
nsv953785 CNV deletion 24416366
nsv961849 CNV duplication 23825009
nsv961850 CNV duplication 23825009
nsv963681 CNV duplication 23825009

Variation tolerance for RGPD4 Gene

Gene Damage Index Score: 12.17; 93.93% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RGPD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RGPD4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RGPD4 Gene

Disorders for RGPD4 Gene

Additional Disease Information for RGPD4

No disorders were found for RGPD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RGPD4 Gene

Publications for RGPD4 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. 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
  4. RSPO-LGR4 functions via IQGAP1 to potentiate Wnt signaling. (PMID: 24639526) Carmon KS … Liu Q (Proceedings of the National Academy of Sciences of the United States of America 2014) 3 58
  5. Mammalian BTBD12/SLX4 assembles a Holliday junction resolvase and is required for DNA repair. (PMID: 19596235) Svendsen JM … Harper JW (Cell 2009) 3 58

Products for RGPD4 Gene

Sources for RGPD4 Gene

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