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Aliases for RGPD6 Gene

Aliases for RGPD6 Gene

  • RANBP2-Like And GRIP Domain Containing 6 2 3 5
  • Ran-Binding Protein 2-Like 1/2 3 4
  • RanBP2-Like 1/2 3 4
  • RanBP2L2 3 4
  • RanBP2L1 3 4
  • RGPD7 3 4
  • RGP6 3 4
  • RANBP2-Like And GRIP Domain-Containing Protein 5/6 3
  • RANBP2-Like And GRIP Domain-Containing Protein 7 3
  • Sperm Membrane Protein BS-63 4
  • RGPD5 RGPD6 4
  • RGP5 4
  • RGP7 4

External Ids for RGPD6 Gene

Previous GeneCards Identifiers for RGPD6 Gene

  • GC02U900804
  • GC02M110708
  • GC02M111271

Summaries for RGPD6 Gene

GeneCards Summary for RGPD6 Gene

RGPD6 (RANBP2-Like And GRIP Domain Containing 6) is a Protein Coding gene. An important paralog of this gene is RGPD5.

Additional gene information for RGPD6 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 RGPD6 Gene

Genomics for RGPD6 Gene

Regulatory Elements for RGPD6 Gene

Enhancers for RGPD6 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02H111429 1.2 Ensembl dbSUPER 28.9 -820.9 -820913 4 HDAC1 PKNOX1 ATF1 FOXA2 ARNT CHAMP1 TCF12 ATF7 CAVIN1 ZBTB2 ANAPC1 RGPD6 ZC3H6 TMEM87B ENSG00000227992 GC02P113411 ENSG00000280878
GH02H111434 1.1 Ensembl dbSUPER 28.9 -829.5 -829513 11 KLF1 ATF1 ETV1 BMI1 PYGO2 ZNF507 RELA YY1 IRF9 ZNF316 ANAPC1 RGPD6 RGPD8 ZC3H6 TMEM87B GC02P113411 ENSG00000280878
GH02H109635 1.5 FANTOM5 Ensembl ENCODE 9.8 +973.6 973636 3 ELF3 FOXA2 MLX ARID4B BATF DNMT3B RARA ATF7 ZNF548 ETV6 SOWAHC SEPT10 RANBP2 RGPD6 GC02P109639
GH02H111184 1 ENCODE 11.8 -575.0 -574971 2 FEZF1 ZNF2 TCF12 GLIS2 KLF7 TSHZ1 ZNF488 NFIL3 ZNF610 ZSCAN16 BCL2L11 RPL22P12 ENSG00000227842 LOC100420892 ANAPC1 RGPD6 ACOXL-AS1 ENSG00000235881 ENSG00000230499 GC02M111153
GH02H111120 1.1 ENCODE 10 -511.1 -511108 4 PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ANAPC1 RGPD6 BCL2L11 PIR45517 GC02M111153
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RGPD6 on UCSC Golden Path with GeneCards custom track

Genomic Location for RGPD6 Gene

Chromosome:
2
Start:
110,513,802 bp from pter
End:
110,610,888 bp from pter
Size:
97,087 bases
Orientation:
Minus strand

Genomic View for RGPD6 Gene

Genes around RGPD6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RGPD6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RGPD6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RGPD6 Gene

Proteins for RGPD6 Gene

  • Protein details for RGPD6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q99666-RGPD5_HUMAN
    Recommended name:
    RANBP2-like and GRIP domain-containing protein 5/6
    Protein Accession:
    Q99666
    Secondary Accessions:
    • Q53QN2
    • Q53T03
    • Q59GM7
    • Q9H0B2

    Protein attributes for RGPD6 Gene

    Size:
    1765 amino acids
    Molecular mass:
    198924 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 RGPD6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RGPD6 Gene

Post-translational modifications for RGPD6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RGPD6 Gene

Domains & Families for RGPD6 Gene

Gene Families for RGPD6 Gene

Suggested Antigen Peptide Sequences for RGPD6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RGPD6: view

No data available for UniProtKB/Swiss-Prot for RGPD6 Gene

Function for RGPD6 Gene

Phenotypes for RGPD6 Gene

GenomeRNAi human phenotypes for RGPD6:
genes like me logo Genes that share phenotypes with RGPD6: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RGPD6 Gene

Localization for RGPD6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RGPD6 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 RGPD6 gene
Compartment Confidence
nucleus 1

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for RGPD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with RGPD6: view

Pathways & Interactions for RGPD6 Gene

SuperPathways for RGPD6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RGPD6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046907 intracellular transport IEA --
genes like me logo Genes that share ontologies with RGPD6: view

No data available for Pathways by source and SIGNOR curated interactions for RGPD6 Gene

Drugs & Compounds for RGPD6 Gene

No Compound Related Data Available

Transcripts for RGPD6 Gene

mRNA/cDNA for RGPD6 Gene

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

Unigene Clusters for RGPD6 Gene

RANBP2-like and GRIP domain containing 6:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RGPD6 Gene

No ASD Table

Relevant External Links for RGPD6 Gene

GeneLoc Exon Structure for
RGPD6
ECgene alternative splicing isoforms for
RGPD6

Expression for RGPD6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RGPD6 Gene

Protein differential expression in normal tissues from HIPED for RGPD6 Gene

This gene is overexpressed in Nasal epithelium (25.0), Testis (21.2), and Ovary (15.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RGPD6 Gene



Protein tissue co-expression partners for RGPD6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RGPD6 Gene:

RGPD6

SOURCE GeneReport for Unigene cluster for RGPD6 Gene:

Hs.645445

mRNA Expression by UniProt/SwissProt for RGPD6 Gene:

Q99666-RGPD5_HUMAN
Tissue specificity: Expressed in testis.

Evidence on tissue expression from TISSUES for RGPD6 Gene

  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with RGPD6: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RGPD6 Gene

Orthologs for RGPD6 Gene

This gene was present in the common ancestor of animals.

Orthologs for RGPD6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia -- 34
  • 96 (a)
ManyToMany
-- 34
  • 96 (a)
ManyToMany
-- 34
  • 92 (a)
ManyToMany
-- 34
  • 82 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Ranbp2 33
  • 87.56 (n)
cow
(Bos Taurus)
Mammalia RANBP2 33
  • 85.03 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 83 (a)
ManyToMany
-- 34
  • 74 (a)
ManyToMany
dog
(Canis familiaris)
Mammalia -- 34
  • 16 (a)
ManyToMany
chicken
(Gallus gallus)
Aves RANBP2 33
  • 70.83 (n)
-- 34
  • 59 (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
  • 66.47 (n)
zebrafish
(Danio rerio)
Actinopterygii si:ch1073-55a19.2 33
  • 56.16 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5071 34
  • 15 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea Y17G9B.4 34
  • 13 (a)
ManyToMany
T22F3.12 34
  • 9 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 5 (a)
OneToMany
Species where no ortholog for RGPD6 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)
  • 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 RGPD6 Gene

ENSEMBL:
Gene Tree for RGPD6 (if available)
TreeFam:
Gene Tree for RGPD6 (if available)

Paralogs for RGPD6 Gene

(7) SIMAP similar genes for RGPD6 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with RGPD6: view

Variants for RGPD6 Gene

Sequence variations from dbSNP and Humsavar for RGPD6 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000031401 -- 110,594,341(+) AAAGC(C/T)TTCCT intron-variant
rs1000493288 -- 110,610,671(+) CGCCC(C/G)TCGCC intron-variant, upstream-variant-2KB
rs1000913825 -- 110,599,236(+) ATATC(A/C)AGGGC intron-variant
rs1000985533 -- 110,601,113(+) ACCTA(C/T)TTCAC intron-variant
rs1001515804 -- 110,608,412(+) AATGG(A/T)TATGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RGPD6 Gene

Variant ID Type Subtype PubMed ID
dgv1162e212 CNV gain 25503493
dgv1163e212 CNV loss 25503493
dgv4037n100 CNV gain 25217958
dgv4047n100 CNV loss 25217958
dgv730e214 CNV gain 21293372
esv2751812 CNV loss 17911159
esv3575292 CNV gain 25503493
esv3584010 CNV loss 25503493
nsv1003103 CNV gain+loss 25217958
nsv1124804 CNV duplication 24896259
nsv1149522 OTHER inversion 26484159
nsv1153351 CNV duplication 26484159
nsv508159 CNV deletion 20534489
nsv510884 OTHER complex 20534489
nsv953789 CNV deletion 24416366
nsv961637 CNV duplication 23825009
nsv961864 CNV duplication 23825009
nsv979088 CNV duplication 23825009

Variation tolerance for RGPD6 Gene

Gene Damage Index Score: 0.01; 0.16% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RGPD6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RGPD6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RGPD6 Gene

Disorders for RGPD6 Gene

Relevant External Links for RGPD6

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RGPD6

No disorders were found for RGPD6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RGPD6 Gene

Publications for RGPD6 Gene

  1. Complex genomic rearrangements lead to novel primate gene function. (PMID: 15710750) Ciccarelli FD … Bork P (Genome research 2005) 2 3 4 60
  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 60
  3. Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis. (PMID: 18220336) Cantin GT … Yates JR (Journal of proteome research 2008) 3 4 60
  4. A quantitative atlas of mitotic phosphorylation. (PMID: 18669648) Dephoure N … Gygi SP (Proceedings of the National Academy of Sciences of the United States of America 2008) 3 4 60
  5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4 60

Products for RGPD6 Gene

Sources for RGPD6 Gene

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