Human Gene RAPGEF6 (ENST00000509018.6_10) from GENCODE V47lift37
  Description: Rap guanine nucleotide exchange factor 6, transcript variant 2 (from RefSeq NM_016340.6)
Gencode Transcript: ENST00000509018.6_10
Gencode Gene: ENSG00000158987.22_18
Transcript (Including UTRs)
   Position: hg19 chr5:130,759,614-130,970,922 Size: 211,309 Total Exon Count: 28 Strand: -
Coding Region
   Position: hg19 chr5:130,762,959-130,970,723 Size: 207,765 Coding Exon Count: 28 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:130,759,614-130,970,922)mRNA (may differ from genome)Protein (1601 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RPGF6_HUMAN
DESCRIPTION: RecName: Full=Rap guanine nucleotide exchange factor 6; AltName: Full=PDZ domain-containing guanine nucleotide exchange factor 2; Short=PDZ-GEF2; AltName: Full=RA-GEF-2;
FUNCTION: Guanine nucleotide exchange factor (GEF) for Rap1A, Rap2A and M-Ras GTPases. Does not interact with cAMP.
SUBUNIT: Interacts with the second PDZ domain of human PTP1e.
SUBCELLULAR LOCATION: Cytoplasm. Cell membrane. Note=Upon binding to M-Ras, it translocates to the plasma membrane.
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.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 1 cyclic nucleotide-binding domain.
SIMILARITY: Contains 1 N-terminal Ras-GEF domain.
SIMILARITY: Contains 1 PDZ (DHR) domain.
SIMILARITY: Contains 1 Ras-associating domain.
SIMILARITY: Contains 1 Ras-GEF domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 11.84 RPKM in Testis
Total median expression: 26.91 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -75.90199-0.381 Picture PostScript Text
3' UTR -808.703345-0.242 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR018490 - cNMP-bd-like
IPR000595 - cNMP-bd_dom
IPR001478 - PDZ
IPR000159 - Ras-assoc
IPR000651 - Ras-like_Gua-exchang_fac_N
IPR008937 - Ras_GEF
IPR023578 - Ras_GEF_dom
IPR001895 - RasGRF_CDC25
IPR014710 - RmlC-like_jellyroll

Pfam Domains:
PF00027 - Cyclic nucleotide-binding domain
PF00595 - PDZ domain
PF00617 - RasGEF domain
PF00618 - RasGEF N-terminal motif
PF00788 - Ras association (RalGDS/AF-6) domain
PF17820 - PDZ domain

SCOP Domains:
48366 - Ras GEF
50156 - PDZ domain-like
51206 - cAMP-binding domain-like
54236 - Ubiquitin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2D93 - NMR MuPIT 3LNY - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q8TEU7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0005515 protein binding
GO:0017016 Ras GTPase binding
GO:0030742 GTP-dependent protein binding
GO:0070300 phosphatidic acid binding

Biological Process:
GO:0007165 signal transduction
GO:0007264 small GTPase mediated signal transduction
GO:0007265 Ras protein signal transduction
GO:0030033 microvillus assembly
GO:0043087 regulation of GTPase activity
GO:0043547 positive regulation of GTPase activity
GO:0072659 protein localization to plasma membrane
GO:0090557 establishment of endothelial intestinal barrier

Cellular Component:
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0030139 endocytic vesicle


-  Descriptions from all associated GenBank mRNAs
  AF117947 - Homo sapiens PDZ domain-containing guanine nucleotide exchange factor I mRNA, complete cds.
LF384728 - JP 2014500723-A/192231: Polycomb-Associated Non-Coding RNAs.
AF478567 - Homo sapiens PDZ domain-containing guanine nucleotide exchange factor PDZ-GEF2 mRNA, complete cds.
AF394782 - Homo sapiens rap guanine nucleotide exchange factor mRNA, complete cds.
BC140820 - Homo sapiens Rap guanine nucleotide exchange factor (GEF) 6, mRNA (cDNA clone MGC:176497 IMAGE:9021688), complete cds.
BC144627 - Homo sapiens Rap guanine nucleotide exchange factor (GEF) 6, mRNA (cDNA clone MGC:178175 IMAGE:9053158), complete cds.
BC133703 - Homo sapiens Rap guanine nucleotide exchange factor (GEF) 6, mRNA (cDNA clone MGC:157029 IMAGE:40124898), complete cds.
KJ898948 - Synthetic construct Homo sapiens clone ccsbBroadEn_08342 RAPGEF6 gene, encodes complete protein.
AF478468 - Homo sapiens Rap1 guanine nucleotide-exchange factor PDZ-GEF2A mRNA, complete cds.
AB527407 - Synthetic construct DNA, clone: pF1KB3463, Homo sapiens RAPGEF6 gene for Rap guanine nucleotide exchange factor (GEF) 6, without stop codon, in Flexi system.
AK074318 - Homo sapiens cDNA FLJ23738 fis, clone HEP15081, highly similar to PDZ domain-containing guanine nucleotide exchange factor I.
AF478469 - Homo sapiens Rap1 guanine nucleotide-exchange factor PDZ-GEF2B mRNA, complete cds.
AK302640 - Homo sapiens cDNA FLJ53249 complete cds, highly similar to Rap guanine nucleotide exchange factor 6.
BC142964 - Homo sapiens Rap guanine nucleotide exchange factor (GEF) 6, mRNA (cDNA clone MGC:167050 IMAGE:8860383), complete cds.
AK056296 - Homo sapiens cDNA FLJ31734 fis, clone NT2RI2007046, highly similar to Homo sapiens PDZ domain-containing guanine nucleotide exchange factor I mRNA.
MA620305 - JP 2018138019-A/192231: Polycomb-Associated Non-Coding RNAs.
AF085846 - Homo sapiens full length insert cDNA clone YI46F09.
AL832899 - Homo sapiens mRNA; cDNA DKFZp667N084 (from clone DKFZp667N084).
LF325860 - JP 2014500723-A/133363: Polycomb-Associated Non-Coding RNAs.
BX649095 - Homo sapiens mRNA; cDNA DKFZp686I15116 (from clone DKFZp686I15116).
JD327822 - Sequence 308846 from Patent EP1572962.
JD430854 - Sequence 411878 from Patent EP1572962.
JD566308 - Sequence 547332 from Patent EP1572962.
JD359643 - Sequence 340667 from Patent EP1572962.
JD110231 - Sequence 91255 from Patent EP1572962.
JD052033 - Sequence 33057 from Patent EP1572962.
JD438666 - Sequence 419690 from Patent EP1572962.
JD564809 - Sequence 545833 from Patent EP1572962.
JD481708 - Sequence 462732 from Patent EP1572962.
LF325859 - JP 2014500723-A/133362: Polycomb-Associated Non-Coding RNAs.
JD296148 - Sequence 277172 from Patent EP1572962.
JD251041 - Sequence 232065 from Patent EP1572962.
JD146694 - Sequence 127718 from Patent EP1572962.
JD525153 - Sequence 506177 from Patent EP1572962.
JD355338 - Sequence 336362 from Patent EP1572962.
JD248289 - Sequence 229313 from Patent EP1572962.
JD078475 - Sequence 59499 from Patent EP1572962.
JD336695 - Sequence 317719 from Patent EP1572962.
JD266715 - Sequence 247739 from Patent EP1572962.
JD066415 - Sequence 47439 from Patent EP1572962.
JD051858 - Sequence 32882 from Patent EP1572962.
JD053434 - Sequence 34458 from Patent EP1572962.
JD442018 - Sequence 423042 from Patent EP1572962.
JD073801 - Sequence 54825 from Patent EP1572962.
JD454190 - Sequence 435214 from Patent EP1572962.
JD288730 - Sequence 269754 from Patent EP1572962.
JD163204 - Sequence 144228 from Patent EP1572962.
JD257849 - Sequence 238873 from Patent EP1572962.
JD233544 - Sequence 214568 from Patent EP1572962.
JD438447 - Sequence 419471 from Patent EP1572962.
JD062400 - Sequence 43424 from Patent EP1572962.
JD371735 - Sequence 352759 from Patent EP1572962.
JD176835 - Sequence 157859 from Patent EP1572962.
JD437997 - Sequence 419021 from Patent EP1572962.
JD265263 - Sequence 246287 from Patent EP1572962.
JD095826 - Sequence 76850 from Patent EP1572962.
JD497588 - Sequence 478612 from Patent EP1572962.
JD358683 - Sequence 339707 from Patent EP1572962.
JD466058 - Sequence 447082 from Patent EP1572962.
JD492594 - Sequence 473618 from Patent EP1572962.
JD525241 - Sequence 506265 from Patent EP1572962.
JD260128 - Sequence 241152 from Patent EP1572962.
LF325854 - JP 2014500723-A/133357: Polycomb-Associated Non-Coding RNAs.
LF325853 - JP 2014500723-A/133356: Polycomb-Associated Non-Coding RNAs.
LF325848 - JP 2014500723-A/133351: Polycomb-Associated Non-Coding RNAs.
MA561437 - JP 2018138019-A/133363: Polycomb-Associated Non-Coding RNAs.
MA561436 - JP 2018138019-A/133362: Polycomb-Associated Non-Coding RNAs.
MA561431 - JP 2018138019-A/133357: Polycomb-Associated Non-Coding RNAs.
MA561430 - JP 2018138019-A/133356: Polycomb-Associated Non-Coding RNAs.
MA561425 - JP 2018138019-A/133351: Polycomb-Associated Non-Coding RNAs.
LF325846 - JP 2014500723-A/133349: Polycomb-Associated Non-Coding RNAs.
LF325845 - JP 2014500723-A/133348: Polycomb-Associated Non-Coding RNAs.
LF325843 - JP 2014500723-A/133346: Polycomb-Associated Non-Coding RNAs.
LF325840 - JP 2014500723-A/133343: Polycomb-Associated Non-Coding RNAs.
LF325839 - JP 2014500723-A/133342: Polycomb-Associated Non-Coding RNAs.
LF325838 - JP 2014500723-A/133341: Polycomb-Associated Non-Coding RNAs.
MA561423 - JP 2018138019-A/133349: Polycomb-Associated Non-Coding RNAs.
MA561422 - JP 2018138019-A/133348: Polycomb-Associated Non-Coding RNAs.
MA561420 - JP 2018138019-A/133346: Polycomb-Associated Non-Coding RNAs.
MA561417 - JP 2018138019-A/133343: Polycomb-Associated Non-Coding RNAs.
MA561416 - JP 2018138019-A/133342: Polycomb-Associated Non-Coding RNAs.
MA561415 - JP 2018138019-A/133341: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A3KN82, A5PLL6, B7ZML2, E9PDV7, ENST00000509018.1, ENST00000509018.2, ENST00000509018.3, ENST00000509018.4, ENST00000509018.5, NM_016340, PDZGEF2, Q8NI21, Q8TEU6, Q8TEU7, Q96PC1, RPGF6_HUMAN, uc323elm.1, uc323elm.2
UCSC ID: ENST00000509018.6_10
RefSeq Accession: NM_016340.6
Protein: Q8TEU7 (aka RPGF6_HUMAN or RGE6_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.