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Aliases for RAPGEF6 Gene

Aliases for RAPGEF6 Gene

  • Rap Guanine Nucleotide Exchange Factor 6 2 3 5
  • PDZ Domain Containing Guanine Nucleotide Exchange Factor (GEF) 2 2 3
  • PDZ Domain-Containing Guanine Nucleotide Exchange Factor 2 3 4
  • Rap Guanine Nucleotide Exchange Factor (GEF) 6 2 3
  • PDZ-GEF2 3 4
  • RA-GEF-2 3 4
  • PDZGEF2 3 4
  • PDZ Domain-Containing Guanine Nucleotide Exchange Factor I 3
  • KIA001LB 3
  • RAGEF2 3

External Ids for RAPGEF6 Gene

Previous HGNC Symbols for RAPGEF6 Gene

  • PDZGEF2

Previous GeneCards Identifiers for RAPGEF6 Gene

  • GC05M130838
  • GC05M130789
  • GC05M125950
  • GC05M130759

Summaries for RAPGEF6 Gene

GeneCards Summary for RAPGEF6 Gene

RAPGEF6 (Rap Guanine Nucleotide Exchange Factor 6) is a Protein Coding gene. Among its related pathways are Ras signaling pathway and Tight junction. Gene Ontology (GO) annotations related to this gene include guanyl-nucleotide exchange factor activity and GTP-dependent protein binding. An important paralog of this gene is ENSG00000273217.

UniProtKB/Swiss-Prot for RAPGEF6 Gene

  • Guanine nucleotide exchange factor (GEF) for Rap1A, Rap2A and M-Ras GTPases. Does not interact with cAMP.

Gene Wiki entry for RAPGEF6 Gene

Additional gene information for RAPGEF6 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAPGEF6 Gene

Genomics for RAPGEF6 Gene

GeneHancer (GH) Regulatory Elements for RAPGEF6 Gene

Promoters and enhancers for RAPGEF6 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
GH05I131629 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 569.3 +1.6 1627 7.3 DMAP1 IRF4 YY1 SLC30A9 SP3 NFYC MEF2D SSRP1 RCOR2 NBN RAPGEF6 MEIKIN LOC102723741 HINT1 CDC42SE2 FNIP1 GC05P131572 ENSG00000273217
GH05I131794 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 11.8 -161.2 -161158 3.6 PKNOX1 CLOCK SMAD1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 FNIP1 ENSG00000279584 ENSG00000273217 IL4 RAD50 ENSG00000224431 RAPGEF6 HINT1 GC05M131666 GC05P131648
GH05I132292 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 6.2 -659.8 -659784 5.2 PKNOX1 SMAD1 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 SLC22A4 P4HA2 RAD50 AFF4 MIR3936HG IL4 FNIP1 ENSG00000202533 MIR3936 SLC22A5
GH05I131513 Enhancer 0.8 Ensembl ENCODE 17 +120.5 120455 2.3 CTCF ZNF316 JUN HMBOX1 ETV6 RUNX3 MAFK EMSY MEIKIN RAPGEF6 LOC102723741 GC05M131544 ENSG00000275939 ENSG00000273217
GH05I131609 Enhancer 1 Ensembl ENCODE 13.3 +25.0 25006 2.4 SOX13 FOXA2 ZNF792 SAP130 JUN ZFP64 ZNF644 RARA ETS1 TEAD3 MEIKIN RAPGEF6 FNIP1 HINT1 GC05P131572 ENSG00000273217
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RAPGEF6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RAPGEF6 gene promoter:

Genomic Locations for RAPGEF6 Gene

Genomic Locations for RAPGEF6 Gene
chr5:131,423,921-131,635,236
(GRCh38/hg38)
Size:
211,316 bases
Orientation:
Minus strand
chr5:130,759,614-130,970,929
(GRCh37/hg19)

Genomic View for RAPGEF6 Gene

Genes around RAPGEF6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAPGEF6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAPGEF6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAPGEF6 Gene

Proteins for RAPGEF6 Gene

  • Protein details for RAPGEF6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TEU7-RPGF6_HUMAN
    Recommended name:
    Rap guanine nucleotide exchange factor 6
    Protein Accession:
    Q8TEU7
    Secondary Accessions:
    • A3KN82
    • A5PLL6
    • B7ZML2
    • E9PDV7
    • Q8NI21
    • Q8TEU6
    • Q96PC1

    Protein attributes for RAPGEF6 Gene

    Size:
    1601 amino acids
    Molecular mass:
    179423 Da
    Quaternary structure:
    • Interacts with the second PDZ domain of human PTP1e.

    Three dimensional structures from OCA and Proteopedia for RAPGEF6 Gene

    Alternative splice isoforms for RAPGEF6 Gene

neXtProt entry for RAPGEF6 Gene

Post-translational modifications for RAPGEF6 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RAPGEF6 Gene

Domains & Families for RAPGEF6 Gene

Gene Families for RAPGEF6 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RAPGEF6: view

No data available for UniProtKB/Swiss-Prot for RAPGEF6 Gene

Function for RAPGEF6 Gene

Molecular function for RAPGEF6 Gene

UniProtKB/Swiss-Prot Function:
Guanine nucleotide exchange factor (GEF) for Rap1A, Rap2A and M-Ras GTPases. Does not interact with cAMP.

Phenotypes From GWAS Catalog for RAPGEF6 Gene

Gene Ontology (GO) - Molecular Function for RAPGEF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IDA 11524421
GO:0005515 protein binding IPI 12095257
GO:0017016 Ras GTPase binding IDA 11524421
GO:0030742 GTP-dependent protein binding IDA 11524421
GO:0070300 phosphatidic acid binding IDA 22797597
genes like me logo Genes that share ontologies with RAPGEF6: view
genes like me logo Genes that share phenotypes with RAPGEF6: view

Animal Models for RAPGEF6 Gene

MGI Knock Outs for RAPGEF6:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RAPGEF6 Gene

Localization for RAPGEF6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAPGEF6 Gene

Cytoplasm. Cell membrane. Note=Upon binding to M-Ras, it translocates to the plasma 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 RAPGEF6 gene
Compartment Confidence
plasma membrane 5
cytosol 5
cytoskeleton 4
nucleus 3
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Centrosome (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RAPGEF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IDA --
GO:0005829 cytosol IDA 22797597
GO:0005886 plasma membrane IEA,IDA 11524421
genes like me logo Genes that share ontologies with RAPGEF6: view

Pathways & Interactions for RAPGEF6 Gene

genes like me logo Genes that share pathways with RAPGEF6: view

Pathways by source for RAPGEF6 Gene

2 KEGG pathways for RAPGEF6 Gene

SIGNOR curated interactions for RAPGEF6 Gene

Activates:

Gene Ontology (GO) - Biological Process for RAPGEF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0007264 small GTPase mediated signal transduction IEA --
GO:0007265 Ras protein signal transduction NAS 11524421
GO:0030033 microvillus assembly IGI 22797597
GO:0043087 regulation of GTPase activity NAS 11524421
genes like me logo Genes that share ontologies with RAPGEF6: view

Drugs & Compounds for RAPGEF6 Gene

(4) Drugs for RAPGEF6 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
cyclic amp Experimental Pharma 0
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with RAPGEF6: view

Transcripts for RAPGEF6 Gene

Unigene Clusters for RAPGEF6 Gene

Rap guanine nucleotide exchange factor (GEF) 6:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RAPGEF6 Gene

No ASD Table

Relevant External Links for RAPGEF6 Gene

GeneLoc Exon Structure for
RAPGEF6
ECgene alternative splicing isoforms for
RAPGEF6

Expression for RAPGEF6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RAPGEF6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RAPGEF6 Gene

This gene is overexpressed in Testis (x17.1).

Protein differential expression in normal tissues from HIPED for RAPGEF6 Gene

This gene is overexpressed in CD8 Tcells (25.9), Peripheral blood mononuclear cells (15.1), and Serum (9.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RAPGEF6 Gene



Protein tissue co-expression partners for RAPGEF6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RAPGEF6 Gene:

RAPGEF6

SOURCE GeneReport for Unigene cluster for RAPGEF6 Gene:

Hs.483329

mRNA Expression by UniProt/SwissProt for RAPGEF6 Gene:

Q8TEU7-RPGF6_HUMAN
Tissue specificity: Isoform 3 has highest expression levels in the brain, heart, liver, lung and placenta and is barely detectable in skeletal muscle, kidney and pancreas.

Evidence on tissue expression from TISSUES for RAPGEF6 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with RAPGEF6: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RAPGEF6 Gene

Orthologs for RAPGEF6 Gene

This gene was present in the common ancestor of animals.

Orthologs for RAPGEF6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RAPGEF6 33 34
  • 99.61 (n)
dog
(Canis familiaris)
Mammalia -- 34
  • 95 (a)
OneToMany
RAPGEF6 33
  • 93.25 (n)
cow
(Bos Taurus)
Mammalia -- 34
  • 93 (a)
OneToMany
RAPGEF6 33
  • 92.65 (n)
mouse
(Mus musculus)
Mammalia Rapgef6 33 16 34
  • 89.15 (n)
rat
(Rattus norvegicus)
Mammalia Rapgef6 33
  • 88.49 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 83 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 81 (a)
OneToMany
chicken
(Gallus gallus)
Aves -- 34
  • 81 (a)
OneToMany
RAPGEF6 33
  • 77.48 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 79 (a)
OneToMany
African clawed frog
(Xenopus laevis)
Amphibia Xl.28320 33
zebrafish
(Danio rerio)
Actinopterygii rapgef6 33 34
  • 65.53 (n)
fruit fly
(Drosophila melanogaster)
Insecta Gef26 34
  • 35 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea pxf-1 33 34
  • 50.48 (n)
Species where no ortholog for RAPGEF6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 RAPGEF6 Gene

ENSEMBL:
Gene Tree for RAPGEF6 (if available)
TreeFam:
Gene Tree for RAPGEF6 (if available)

Paralogs for RAPGEF6 Gene

Pseudogenes.org Pseudogenes for RAPGEF6 Gene

genes like me logo Genes that share paralogs with RAPGEF6: view

Variants for RAPGEF6 Gene

Sequence variations from dbSNP and Humsavar for RAPGEF6 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000007553 -- 131,570,794(-) G/A intron_variant
rs1000012867 -- 131,583,886(-) A/C intron_variant
rs1000021388 -- 131,441,664(-) C/T genic_downstream_transcript_variant, intron_variant
rs1000025536 -- 131,607,953(-) G/A intron_variant
rs1000032886 -- 131,567,988(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RAPGEF6 Gene

Variant ID Type Subtype PubMed ID
esv1452882 CNV insertion 17803354
esv2586698 CNV deletion 19546169
esv2730774 CNV deletion 23290073
esv2730775 CNV deletion 23290073
esv2730776 CNV deletion 23290073
esv2730777 CNV deletion 23290073
esv2730778 CNV deletion 23290073
esv2730779 CNV deletion 23290073
esv3284 CNV loss 18987735
esv3305100 CNV mobile element insertion 20981092
esv3309221 CNV mobile element insertion 20981092
esv3566653 CNV deletion 23714750
esv3575881 CNV gain 25503493
esv3606794 CNV loss 21293372
esv3606795 CNV gain 21293372
nsv1024789 CNV loss 25217958
nsv1032888 CNV loss 25217958
nsv1117578 CNV deletion 24896259
nsv1128189 CNV deletion 24896259
nsv509993 OTHER sequence alteration 20534489

Variation tolerance for RAPGEF6 Gene

Residual Variation Intolerance Score: 1.78% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.02; 0.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAPGEF6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAPGEF6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAPGEF6 Gene

Disorders for RAPGEF6 Gene

Additional Disease Information for RAPGEF6

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RAPGEF6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RAPGEF6 Gene

Publications for RAPGEF6 Gene

  1. Identification and characterization of RA-GEF-2, a Rap guanine nucleotide exchange factor that serves as a downstream target of M-Ras. (PMID: 11524421) Gao X … Kataoka T (The Journal of biological chemistry 2001) 2 3 4 58
  2. Junctional adhesion molecule A interacts with Afadin and PDZ-GEF2 to activate Rap1A, regulate beta1 integrin levels, and enhance cell migration. (PMID: 19176753) Severson EA … Parkos CA (Molecular biology of the cell 2009) 3 22 58
  3. Interaction between interleukin 3 and dystrobrevin-binding protein 1 in schizophrenia. (PMID: 18804346) Edwards TL … Chen X (Schizophrenia research 2008) 3 44 58
  4. Association of haplotypes spanning PDZ-GEF2, LOC728637 and ACSL6 with schizophrenia in Han Chinese. (PMID: 18718982) Luo XJ … Su B (Journal of medical genetics 2008) 3 44 58
  5. Characterisation of PDZ-GEFs, a family of guanine nucleotide exchange factors specific for Rap1 and Rap2. (PMID: 12581858) Kuiperij HB … Zwartkruis FJ (Biochimica et biophysica acta 2003) 3 4 58

Products for RAPGEF6 Gene

Sources for RAPGEF6 Gene

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