Human Gene RAP1A (ENST00000369709.4_4) from GENCODE V47lift37
  Description: RAP1A, member of RAS oncogene family, transcript variant 2 (from RefSeq NM_002884.4)
Gencode Transcript: ENST00000369709.4_4
Gencode Gene: ENSG00000116473.15_7
Transcript (Including UTRs)
   Position: hg19 chr1:112,162,411-112,259,313 Size: 96,903 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr1:112,233,983-112,251,857 Size: 17,875 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:112,162,411-112,259,313)mRNA (may differ from genome)Protein (184 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RAP1A_HUMAN
DESCRIPTION: RecName: Full=Ras-related protein Rap-1A; AltName: Full=C21KG; AltName: Full=G-22K; AltName: Full=GTP-binding protein smg p21A; AltName: Full=Ras-related protein Krev-1; Flags: Precursor;
FUNCTION: Induces morphological reversion of a cell line transformed by a Ras oncogene. Counteracts the mitogenic function of Ras, at least partly because it can interact with Ras GAPs and RAF in a competitive manner.
ENZYME REGULATION: Activated by guanine nucleotide-exchange factors (GEF) EPAC and EPAC2 in a cAMP-dependent manner, and GFR.
SUBUNIT: In its GTP-bound form interacts with PLCE1 and RADIL. Interacts with SGSM1, SGSM2 and SGSM3.
INTERACTION: P04049:RAF1; NbExp=2; IntAct=EBI-491414, EBI-365996; Q8WWW0-2:RASSF5; NbExp=3; IntAct=EBI-491414, EBI-960502; Q5EBH1:Rassf5 (xeno); NbExp=2; IntAct=EBI-491414, EBI-960530;
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor.
SIMILARITY: Belongs to the small GTPase superfamily. Ras family.
SEQUENCE CAUTION: Sequence=CAB55685.2; Type=Erroneous gene model prediction;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/RAP1AID272.html";

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: RAP1A
Diseases sorted by gene-association score: kabuki syndrome 1* (205), leukocyte adhesion deficiency, type iii (10), tuberous sclerosis (9), babesiosis (8), central nervous system hemangioma (7), cerebral cavernous malformations-1 (6), cerebral cavernous malformations-2 (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 41.75 RPKM in Colon - Sigmoid
Total median expression: 803.50 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 -71.70173-0.414 Picture PostScript Text
3' UTR -1061.604290-0.247 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
IPR005225 - Small_GTP-bd_dom
IPR001806 - Small_GTPase
IPR020849 - Small_GTPase_Ras

Pfam Domains:
PF00025 - ADP-ribosylation factor family
PF00071 - Ras family
PF08477 - Ras of Complex, Roc, domain of DAPkinase

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1C1Y - X-ray MuPIT 1GUA - X-ray MuPIT 3KUC - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P62834
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    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003924 GTPase activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0008565 protein transporter activity
GO:0017016 Ras GTPase binding
GO:0017034 Rap guanyl-nucleotide exchange factor activity
GO:0044877 macromolecular complex binding

Biological Process:
GO:0007165 signal transduction
GO:0007264 small GTPase mediated signal transduction
GO:0007399 nervous system development
GO:0009743 response to carbohydrate
GO:0010976 positive regulation of neuron projection development
GO:0015031 protein transport
GO:0032486 Rap protein signal transduction
GO:0032966 negative regulation of collagen biosynthetic process
GO:0035690 cellular response to drug
GO:0038180 nerve growth factor signaling pathway
GO:0043312 neutrophil degranulation
GO:0043547 positive regulation of GTPase activity
GO:0045860 positive regulation of protein kinase activity
GO:0046326 positive regulation of glucose import
GO:0050796 regulation of insulin secretion
GO:0061028 establishment of endothelial barrier
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071320 cellular response to cAMP
GO:0071333 cellular response to glucose stimulus
GO:0071407 cellular response to organic cyclic compound
GO:0097327 response to antineoplastic agent
GO:0097421 liver regeneration
GO:1901888 regulation of cell junction assembly
GO:1905451 positive regulation of Fc-gamma receptor signaling pathway involved in phagocytosis
GO:1990090 cellular response to nerve growth factor stimulus
GO:2000301 negative regulation of synaptic vesicle exocytosis
GO:2001214 positive regulation of vasculogenesis
GO:0030033 microvillus assembly

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005770 late endosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030054 cell junction
GO:0032045 guanyl-nucleotide exchange factor complex
GO:0035579 specific granule membrane
GO:0043005 neuron projection
GO:0043209 myelin sheath
GO:0045335 phagocytic vesicle
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  KJ891980 - Synthetic construct Homo sapiens clone ccsbBroadEn_01374 RAP1A gene, encodes complete protein.
E02296 - DNA encoding cancer suppressor gene Krev-1.
M22995 - Human ras-related protein (Krev-1) mRNA, complete cds.
BC014086 - Homo sapiens RAP1A, member of RAS oncogene family, mRNA (cDNA clone MGC:20027 IMAGE:4422971), complete cds.
AK293044 - Homo sapiens cDNA FLJ75985 complete cds, highly similar to Homo sapiens RAP1A, member of RAS oncogene family (RAP1A), transcript variant 2, mRNA.
X12533 - Human rap1A mRNA for ras-related protein.
EU831467 - Synthetic construct Homo sapiens clone HAIB:100066496; DKFZo008F0917 RAP1A, member of RAS oncogene family protein (RAP1A) gene, encodes complete protein.
EU831554 - Synthetic construct Homo sapiens clone HAIB:100066583; DKFZo004F0918 RAP1A, member of RAS oncogene family protein (RAP1A) gene, encodes complete protein.
AB464127 - Synthetic construct DNA, clone: pF1KB6804, Homo sapiens RAP1A gene for RAP1A, member of RAS oncogene family, without stop codon, in Flexi system.
AB451360 - Homo sapiens RAP1A mRNA for Ras-related protein Rap-1A precursor, partial cds, clone: FLJ08033AAAF.
AB451235 - Homo sapiens RAP1A mRNA for Ras-related protein Rap-1A precursor, complete cds, clone: FLJ08033AAAN.
AF493912 - Homo sapiens Ras family small GTP binding protein RAP1A (RAP1A) mRNA, complete cds.
BT019666 - Homo sapiens RAP1A, member of RAS oncogene family mRNA, complete cds.
JD296739 - Sequence 277763 from Patent EP1572962.
JD155389 - Sequence 136413 from Patent EP1572962.
JD093979 - Sequence 75003 from Patent EP1572962.
AK094737 - Homo sapiens cDNA FLJ37418 fis, clone BRAWH2000488.
LF206284 - JP 2014500723-A/13787: Polycomb-Associated Non-Coding RNAs.
LF352980 - JP 2014500723-A/160483: Polycomb-Associated Non-Coding RNAs.
AK023457 - Homo sapiens cDNA FLJ13395 fis, clone PLACE1001311.
MA588557 - JP 2018138019-A/160483: Polycomb-Associated Non-Coding RNAs.
MA441861 - JP 2018138019-A/13787: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_integrinPathway - Integrin Signaling Pathway
h_metPathway - Signaling of Hepatocyte Growth Factor Receptor

Reactome (by CSHL, EBI, and GO)

Protein P62834 (Reactome details) participates in the following event(s):

R-HSA-169904 C3G stimulates nucleotide exchange on Rap1
R-HSA-170965 (Frs2)Rap1-GTP binds to and activates B-Raf
R-HSA-170979 (Frs2)C3G stimulates nucleotide exchange on Rap1
R-HSA-381727 RAP1A exchanges GDP for GTP
R-HSA-6799350 Exocytosis of specific granule membrane proteins
R-HSA-169901 (ARMS)Rap1-GTP binds and activates B-Raf
R-HSA-354173 Activation of Rap1 by cytosolic GEFs
R-HSA-939265 Activation of Rap1 by membrane-associated GEFs
R-HSA-8875568 RAPGEF1 activates RAP1
R-HSA-392513 Rap1 signal termination by Rap1GAPs
R-HSA-354060 Translocation of RIAM to plasma membrane
R-HSA-392835 Rap1 sequesters Raf1 to inhibit ERK cascade
R-HSA-354097 Activation of Talin
R-HSA-354077 Integrin alphaIIb beta3 activation
R-HSA-354149 Interaction of integrin alphaIIb beta3 with Fibrinogen
R-HSA-432096 Activated integrin alphaIIb beta3 binds SHC1
R-HSA-377643 Dephosphorylation of inactive SRC by PTPB1
R-HSA-377644 Release of CSK from SRC
R-HSA-377641 Clustering of Integrin alphaIIb beta3 complexes
R-HSA-377640 Autophosphorylation of SRC
R-HSA-354066 Translocation of FADK1 to Focal complexes
R-HSA-429415 SYK binds to integrin alphaIIb beta3
R-HSA-354087 Recruitment of GRB2 to p-FADK1
R-HSA-372705 Recruitment of p130Cas to FADK1
R-HSA-354124 Phosphorylation of pFADK1 by SRC
R-HSA-354073 Autophosphorylation of FADK1 at Y397
R-HSA-429441 SYK activation by SRC
R-HSA-354165 Interaction of SOS with GRB2 bound to FADK1
R-HSA-372697 Crk binding to p130cas
R-HSA-372693 Phosphorylation of p130Cas by SRC-FADK1 complex
R-HSA-5672972 MAP2Ks and MAPKs bind to the activated RAF complex
R-HSA-6802912 High kinase activity BRAF mutants bind MAP2Ks and MAPKs
R-HSA-6802914 RAS:GTP:moderate kinase activity p-RAF complexes bind MAP2Ks and MAPKs
R-HSA-6802925 Mutant RAS:p-RAF complexes bind MAP2Ks and MAPKs
R-HSA-6802934 p-BRAF and RAF fusion dimers bind MAP2Ks and MAPKs
R-HSA-6802942 RAS:GTP:p-RAF complexes paradoxically bind MAP2Ks and MAPKs
R-HSA-5672980 Dissociation of RAS:RAF complex
R-HSA-6802932 Dissociation of BRAF/RAF fusion complex
R-HSA-6803227 Dissociation of high activity BRAF complexes
R-HSA-6803230 Dissociation of moderate activity BRAF complexes
R-HSA-6803233 Dissociation of oncogenic RAS:RAF complex
R-HSA-6803234 Dissociation of paradoxically activated RAS:BRAF complexes
R-HSA-5672978 RAF phosphorylates MAP2K dimer
R-HSA-5672973 MAP2Ks phosphorylate MAPKs
R-HSA-6802918 Activated MAP2Ks phosphorylate MAPKs downstream of inactive BRAF mutants
R-HSA-6802943 RAS:GTP:inactive p-RAF complexes phosphorylate MAP2Ks
R-HSA-6802919 RAS:GTP:moderate kinase activity p-RAF complexes phosphorylate MAP2Ks
R-HSA-6802921 Activated MAP2Ks phosphorylate MAPKs downstream of moderate kinase activity BRAF mutants
R-HSA-6802911 High kinase activity BRAF complexes phosphorylate MAP2Ks
R-HSA-6802910 Activated MAP2Ks phosphorylate MAPKs downstream of high kinase activity BRAF mutants
R-HSA-6802926 Mutant RAS:p-RAF complexes phosphorylate MAP2Ks
R-HSA-6802922 Activated MAP2Ks phosphorylate MAPKs downstream of oncogenic RAS
R-HSA-6802933 p-BRAF and RAF fusion dimers phosphorylate MAP2Ks
R-HSA-6802935 MAPKs are phosphorylated downstream of BRAF and RAF fusion dimers
R-HSA-170984 ARMS-mediated activation
R-HSA-170968 Frs2-mediated activation
R-HSA-381676 Glucagon-like Peptide-1 (GLP1) regulates insulin secretion
R-HSA-6798695 Neutrophil degranulation
R-HSA-169893 Prolonged ERK activation events
R-HSA-422356 Regulation of insulin secretion
R-HSA-354192 Integrin alphaIIb beta3 signaling
R-HSA-392517 Rap1 signalling
R-HSA-8875555 MET activates RAP1 and RAC1
R-HSA-168249 Innate Immune System
R-HSA-187687 Signalling to ERKs
R-HSA-163685 Energy Metabolism
R-HSA-76009 Platelet Aggregation (Plug Formation)
R-HSA-9006921 Integrin signaling
R-HSA-1280218 Adaptive Immune System
R-HSA-8875878 MET promotes cell motility
R-HSA-168256 Immune System
R-HSA-187037 Signaling by NTRK1 (TRKA)
R-HSA-1430728 Metabolism
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-162582 Signal Transduction
R-HSA-6806834 Signaling by MET
R-HSA-166520 Signaling by NTRKs
R-HSA-109582 Hemostasis
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-354194 GRB2:SOS provides linkage to MAPK signaling for Integrins
R-HSA-372708 p130Cas linkage to MAPK signaling for integrins
R-HSA-5674135 MAP2K and MAPK activation
R-HSA-6802948 Signaling by high-kinase activity BRAF mutants
R-HSA-6802946 Signaling by moderate kinase activity BRAF mutants
R-HSA-6802949 Signaling by RAS mutants
R-HSA-6802952 Signaling by BRAF and RAF fusions
R-HSA-6802955 Paradoxical activation of RAF signaling by kinase inactive BRAF
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-6802957 Oncogenic MAPK signaling
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-5663202 Diseases of signal transduction
R-HSA-5683057 MAPK family signaling cascades
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000369709.1, ENST00000369709.2, ENST00000369709.3, KREV1, NM_002884, P10113, P62834, RAP1A_HUMAN, uc318huc.1, uc318huc.2
UCSC ID: ENST00000369709.4_4
RefSeq Accession: NM_002884.4
Protein: P62834 (aka RAP1A_HUMAN or RAPA_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.