Aliases for RGPD4 Gene

Aliases for RGPD4 Gene

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

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. Diseases associated with RGPD4 include Asperger Syndrome. 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 Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification 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
GH02J107826 Promoter 0.7 EPDnew Ensembl 770.9 +2.1 2069 4.4 RGPD4 RGPD4-AS1 piR-44301-002
GH02J108532 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 4.5 +708.7 708652 6 ZBTB40 ZBTB6 RBPJ POLR2A NR2F6 MIXL1 ZNF362 HLF L3MBTL2 DACH1 GCC2-AS1 LIMS1 GCC2 SULT1C4 RGPD4 lnc-LIMS1-1 LIMS3-LOC440895
GH02J107987 Promoter 0.8 EPDnew Ensembl 9.4 +159.8 159768 0.6 EZH2 SIN3A SLC5A7 lnc-RGPD4-4 RGPD4 piR-61539-006
GH02J108570 Enhancer 1.1 Ensembl ENCODE dbSUPER 4.1 +747.2 747238 8.1 POLR2A RELA ZNF121 ZNF687 PRDM1 ZBED1 IKZF1 TRIM22 IKZF2 CEBPB GCC2 LINC01594 LIMS1-AS1 SULT1C4 RGPD4 LIMS1 LIMS3-LOC440895
GH02J108313 Enhancer 0.7 ENCODE 5 +488.8 488799 3.6 ZNF121 MAFK PRDM10 ZNF7 ZNF316 NRF1 SOX13 MAFG SAP130 TEAD1 SULT1C2P2 lnc-SULT1C2-2 piR-57122 SULT1C2 LINC01594 RGPD4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RGPD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RGPD4 gene promoter:
  • aMEF-2
  • IRF-1
  • MEF-2
  • MEF-2A
  • Nkx2-5
  • RORalpha2
  • Sp1

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)
Size:
65,613 bases
Orientation:
Plus strand

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

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

GenScript: Design optimal peptide antigens:
  • cDNA FLJ59078, highly similar to Ran-binding protein 2-like 6 (B4DZH4_HUMAN)
  • RanBP2-like and GRIP domain-containing protein 4 (RGPD4_HUMAN)
genes like me logo Genes that share domains with RGPD4: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RGPD4 Gene

Function for RGPD4 Gene

Phenotypes From GWAS Catalog 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 21873635
GO:0005515 protein binding IEA --
GO:0008536 Ran GTPase binding IBA 21873635
genes like me logo Genes that share ontologies with RGPD4: view
genes like me logo Genes that share phenotypes with RGPD4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RGPD4

No data available for Molecular function , Enzyme Numbers (IUBMB) , 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
cytosol 3
plasma membrane 0
mitochondrion 0
peroxisome 0

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 21873635
GO:0005643 nuclear pore IBA 21873635
GO:0005737 cytoplasm IBA 21873635
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

PathCards logo

SuperPathways for RGPD4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RGPD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006607 NLS-bearing protein import into nucleus IBA 21873635
GO:0043547 positive regulation of GTPase activity IEA --
GO:0046907 intracellular transport IEA --
genes like me logo Genes that share ontologies with RGPD4: view

No data available for Pathways by source and 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

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RGPD4

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, 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 -- 33
  • 96 (a)
ManyToMany
-- 33
  • 96 (a)
ManyToMany
-- 33
  • 90 (a)
ManyToMany
-- 33
  • 82 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Ranbp2 32
  • 87.87 (n)
cow
(Bos Taurus)
Mammalia RANBP2 32
  • 85.26 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 33
  • 82 (a)
ManyToMany
-- 33
  • 76 (a)
ManyToMany
chicken
(Gallus gallus)
Aves RANBP2 32
  • 71.02 (n)
-- 33
  • 60 (a)
ManyToMany
-- 33
  • 48 (a)
ManyToMany
-- 33
  • 44 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 33
  • 42 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia ranbp2 32
  • 66.69 (n)
zebrafish
(Danio rerio)
Actinopterygii si:ch1073-55a19.2 32
  • 56.71 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5071 33
  • 14 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y17G9B.4 33
  • 13 (a)
ManyToMany
T22F3.12 33
  • 7 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 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

Paralogs for RGPD4 Gene

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

  • RGPD4_HUMAN
  • J3KNY6_HUMAN
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
rs1306583979 not-provided, not provided 107,859,172(+) G/A coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs1000017831 -- 107,836,132(+) G/A intron_variant
rs1000018256 -- 107,855,354(+) C/T intron_variant
rs1000149172 -- 107,845,544(+) G/C 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

SNP Genotyping and Copy Number Assay Products

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

Disorders for RGPD4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RGPD4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
asperger syndrome
  • asperger disorder
- elite association - COSMIC cancer census association via MalaCards
Search RGPD4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RGPD4

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

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

Publications for RGPD4 Gene

  1. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 2 3 4 56
  2. Complex genomic rearrangements lead to novel primate gene function. (PMID: 15710750) Ciccarelli FD … Bork P (Genome research 2005) 2 3 4 56
  3. ∆F508 CFTR interactome remodelling promotes rescue of cystic fibrosis. (PMID: 26618866) Pankow S … Yates JR (Nature 2015) 3 56
  4. 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 56
  5. 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 56

Products for RGPD4 Gene

Sources for RGPD4 Gene