Aliases for RGP1 Gene

Aliases for RGP1 Gene

  • RGP1 Homolog, RAB6A GEF Complex Partner 1 2 3 5
  • KIAA0258 2 3 4
  • Retrograde Golgi Transport Protein RGP1 Homolog 3 4
  • RAB6A-GEF Complex Partner Protein 2 3 4
  • RGP1 Retrograde Golgi Transport Homolog (S. Cerevisiae) 2
  • RGP1 Retrograde Golgi Transport Homolog 3
  • RGP1 5

External Ids for RGP1 Gene

Previous HGNC Symbols for RGP1 Gene

  • KIAA0258

Previous GeneCards Identifiers for RGP1 Gene

  • GC09P035740

Summaries for RGP1 Gene

GeneCards Summary for RGP1 Gene

RGP1 (RGP1 Homolog, RAB6A GEF Complex Partner 1) is a Protein Coding gene. Among its related pathways are Retrograde transport at the Trans-Golgi-Network and Vesicle-mediated transport. Gene Ontology (GO) annotations related to this gene include Rab GTPase binding and Rab guanyl-nucleotide exchange factor activity.

UniProtKB/Swiss-Prot Summary for RGP1 Gene

  • The RIC1-RGP1 complex acts as a guanine nucleotide exchange factor (GEF), which activates RAB6A by exchanging bound GDP for free GTP and may thereby required for efficient fusion of endosome-derived vesicles with the Golgi compartment. The RIC1-RGP1 complex participates in the recycling of mannose-6-phosphate receptors.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RGP1 Gene

Genomics for RGP1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RGP1 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
GH09J035745 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 -1.0 -1005 5.4 POLR2A ZBTB10 YY1 NONO ZNF592 SMAD5 SIN3A ELK1 ETS1 ZNF341 GBA2 RGP1 NPR2 SPAG8 HINT2 TMEM8B TPM2 lnc-MSMP-3 HSALNG0070949 CREB3
GH09J034987 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.9 -756.0 -756007 10.6 SP1 ZNF654 ZNF207 MYC NCOR1 IKZF1 SIX5 JUND ZNF592 ATF2 DNAJB5 DNAJB5-DT VCP ARHGEF39 TPM2 FANCG UBAP2 FAM219A CCDC107 TLN1
GH09J035679 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.9 -63.1 -63117 12.9 IKZF1 JUND ATF2 POLR2A ZIC2 SMAD5 ZNF341 MNT NR2C1 MAX TPM2 GBA2 TMEM8B TLN1 NPR2 CCDC107 SIT1 CREB3 RGP1 ENSG00000228843
GH09J035755 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 10.2 +8.1 8133 3.8 BCLAF1 MYC IKZF1 ZNF580 POLR2A ZNF223 ZBTB10 MXD4 CTCF SIN3A NPR2 ENSG00000228843 MSMP lnc-MSMP-2 PIGO ARHGEF39 TMEM8B TPM2 CCDC107 TLN1
GH09J035616 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE dbSUPER 10.4 -130.0 -130033 6.4 BCLAF1 JUND POLR2A ZIC2 BCL11A ETS1 SIN3A GABPA RFX5 EBF1 CD72 CCDC107 RN7SL22P ARHGEF39 SIT1 CA9 FAM166B CREB3 TLN1 GBA2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RGP1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RGP1

Top Transcription factor binding sites by QIAGEN in the RGP1 gene promoter:
  • AP-1
  • AP-2alpha
  • AP-2alpha isoform 2
  • AP-2alpha isoform 3
  • AP-2alpha isoform 4
  • AP-2alphaA
  • c-Ets-1
  • Nkx2-5
  • Pax-6

Genomic Locations for RGP1 Gene

Latest Assembly
chr9:35,749,287-35,758,585
(GRCh38/hg38)
Size:
9,299 bases
Orientation:
Plus strand

Previous Assembly
chr9:35,749,284-35,758,582
(GRCh37/hg19 by Entrez Gene)
Size:
9,299 bases
Orientation:
Plus strand

chr9:35,749,203-35,758,572
(GRCh37/hg19 by Ensembl)
Size:
9,370 bases
Orientation:
Plus strand

Genomic View for RGP1 Gene

Genes around RGP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RGP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RGP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RGP1 Gene

Proteins for RGP1 Gene

  • Protein details for RGP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92546-RGP1_HUMAN
    Recommended name:
    RAB6A-GEF complex partner protein 2
    Protein Accession:
    Q92546
    Secondary Accessions:
    • Q5TCV5

    Protein attributes for RGP1 Gene

    Size:
    391 amino acids
    Molecular mass:
    42455 Da
    Quaternary structure:
    • Forms a complex with RIC1; the interaction enhances RAB6A GTPase activity. Interacts with RIC1. Interacts with RAB6A; the interaction is direct with a preference for RAB6A-GDP. Interacts with RAB33B.
    SequenceCaution:
    • Sequence=BAA13388.2; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for RGP1 Gene

Post-translational modifications for RGP1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RGP1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RGP1 Gene

Domains & Families for RGP1 Gene

Gene Families for RGP1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RGP1 Gene

InterPro:

Suggested Antigen Peptide Sequences for RGP1 Gene

GenScript: Design optimal peptide antigens:
  • Retrograde Golgi transport protein RGP1 homolog (RGP1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q92546

UniProtKB/Swiss-Prot:

RGP1_HUMAN :
  • Belongs to the RGP1 family.
Family:
  • Belongs to the RGP1 family.
genes like me logo Genes that share domains with RGP1: view

Function for RGP1 Gene

Molecular function for RGP1 Gene

UniProtKB/Swiss-Prot Function:
The RIC1-RGP1 complex acts as a guanine nucleotide exchange factor (GEF), which activates RAB6A by exchanging bound GDP for free GTP and may thereby required for efficient fusion of endosome-derived vesicles with the Golgi compartment. The RIC1-RGP1 complex participates in the recycling of mannose-6-phosphate receptors.

Phenotypes From GWAS Catalog for RGP1 Gene

Gene Ontology (GO) - Molecular Function for RGP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IBA,IDA 23091056
GO:0005515 protein binding IPI 22458338
GO:0031267 small GTPase binding IDA 23091056
genes like me logo Genes that share ontologies with RGP1: view
genes like me logo Genes that share phenotypes with RGP1: view

Animal Models for RGP1 Gene

MGI Knock Outs for RGP1:
  • Rgp1 Rgp1<tm1.1(KOMP)Vlcg>

miRNA for RGP1 Gene

miRTarBase miRNAs that target RGP1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RGP1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RGP1 Gene

Localization for RGP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RGP1 Gene

Cytoplasm, cytosol. Membrane.

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 RGP1 gene
Compartment Confidence
cytosol 5
golgi apparatus 5
plasma membrane 4
mitochondrion 2
peroxisome 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RGP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0005886 plasma membrane IDA --
GO:0016020 membrane IEA,IDA 23091056
genes like me logo Genes that share ontologies with RGP1: view

Pathways & Interactions for RGP1 Gene

genes like me logo Genes that share pathways with RGP1: view

Gene Ontology (GO) - Biological Process for RGP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042147 retrograde transport, endosome to Golgi IBA,IMP 23091056
GO:0043547 positive regulation of GTPase activity IDA 23091056
GO:1903363 negative regulation of cellular protein catabolic process IMP 23091056
genes like me logo Genes that share ontologies with RGP1: view

No data available for SIGNOR curated interactions for RGP1 Gene

Drugs & Compounds for RGP1 Gene

No Compound Related Data Available

Transcripts for RGP1 Gene

mRNA/cDNA for RGP1 Gene

1 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RGP1

Alternative Splicing Database (ASD) splice patterns (SP) for RGP1 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10
SP1:
SP2:
SP3:

Relevant External Links for RGP1 Gene

GeneLoc Exon Structure for
RGP1

Expression for RGP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RGP1 Gene

Protein differential expression in normal tissues from HIPED for RGP1 Gene

This gene is overexpressed in Heart (34.1), Placenta (21.3), and Liver (13.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RGP1 Gene



Protein tissue co-expression partners for RGP1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RGP1

SOURCE GeneReport for Unigene cluster for RGP1 Gene:

Hs.493804

Evidence on tissue expression from TISSUES for RGP1 Gene

  • Lung(4.2)
  • Bone marrow(4.1)
  • Nervous system(2.4)
genes like me logo Genes that share expression patterns with RGP1: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RGP1 Gene

Orthologs for RGP1 Gene

This gene was present in the common ancestor of animals.

Orthologs for RGP1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RGP1 29 30
  • 99.49 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RGP1 30
  • 93 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia RGP1 29 30
  • 91.99 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RGP1 29 30
  • 90.94 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rgp1 29
  • 89.86 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia RGP1 30
  • 89 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Rgp1 29 16 30
  • 88.83 (n)
OneToOne
Chicken
(Gallus gallus)
Aves RGP1 29 30
  • 70.89 (n)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.17737 29
Zebrafish
(Danio rerio)
Actinopterygii rgp1 29 30
  • 65.11 (n)
OneToOne
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10152 29
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003042 29
  • 49.14 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG1116 29 30
  • 48.5 (n)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea M01F1.9 29 30
  • 41.17 (n)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.2444 30
  • 43 (a)
OneToOne
Species where no ortholog for RGP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for RGP1 Gene

ENSEMBL:
Gene Tree for RGP1 (if available)
TreeFam:
Gene Tree for RGP1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RGP1: view image
Alliance of Genome Resources:
Additional Orthologs for RGP1

Paralogs for RGP1 Gene

No data available for Paralogs for RGP1 Gene

Variants for RGP1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RGP1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RGP1 Gene

Variant ID Type Subtype PubMed ID
nsv1125318 OTHER inversion 24896259

Variation tolerance for RGP1 Gene

Residual Variation Intolerance Score: 36.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.40; 54.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RGP1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RGP1
Leiden Open Variation Database (LOVD)
RGP1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RGP1 Gene

Disorders for RGP1 Gene

Additional Disease Information for RGP1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for RGP1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RGP1 Gene

Publications for RGP1 Gene

  1. Ric1-Rgp1 complex is a guanine nucleotide exchange factor for the late Golgi Rab6A GTPase and an effector of the medial Golgi Rab33B GTPase. (PMID: 23091056) Pusapati GV … Pfeffer SR (The Journal of biological chemistry 2012) 2 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PMID: 9039502) Nagase T … Nomura N (DNA research : an international journal for rapid publication of reports on genes and genomes 1996) 3 4
  4. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  5. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. (PMID: 29568061) Liu X … Varjosalo M (Nature communications 2018) 3

Products for RGP1 Gene

Sources for RGP1 Gene