Human Gene RASGEF1A (ENST00000395810.6) from GENCODE V44
  Description: Homo sapiens RasGEF domain family member 1A (RASGEF1A), transcript variant 2, mRNA. (from RefSeq NM_145313)
Gencode Transcript: ENST00000395810.6
Gencode Gene: ENSG00000198915.12
Transcript (Including UTRs)
   Position: hg38 chr10:43,194,535-43,267,065 Size: 72,531 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg38 chr10:43,196,244-43,206,116 Size: 9,873 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:43,194,535-43,267,065)mRNA (may differ from genome)Protein (481 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RGF1A_HUMAN
DESCRIPTION: RecName: Full=Ras-GEF domain-containing family member 1A;
FUNCTION: Guanine nucleotide exchange factor (GEF) with specificity for RAP2A, KRAS, HRAS, and NRAS (in vitro). Plays a role in cell migration.
TISSUE SPECIFICITY: Detected in brain and spinal cord. Highly expressed in a number of intrahepatic cholangiocarcinoma tissue biopsies.
SIMILARITY: Contains 1 N-terminal Ras-GEF 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


-  MalaCards Disease Associations
  MalaCards Gene Search: RASGEF1A
Diseases sorted by gene-association score: intrahepatic cholangiocarcinoma (5), hirschsprung disease 1 (1)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.81 RPKM in Brain - Cortex
Total median expression: 103.79 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 -156.70227-0.690 Picture PostScript Text
3' UTR -570.101709-0.334 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
IPR000651 - Ras-like_Gua-exchang_fac_N
IPR008937 - Ras_GEF
IPR023578 - Ras_GEF_dom
IPR001895 - RasGRF_CDC25

Pfam Domains:
PF00617 - RasGEF domain
PF00618 - RasGEF N-terminal motif

ModBase Predicted Comparative 3D Structure on Q8N9B8
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005085 guanyl-nucleotide exchange factor activity
GO:0005088 Ras guanyl-nucleotide exchange factor activity

Biological Process:
GO:0000165 MAPK cascade
GO:0007264 small GTPase mediated signal transduction
GO:0016477 cell migration
GO:0046579 positive regulation of Ras protein signal transduction

Cellular Component:
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC022548 - Homo sapiens RasGEF domain family, member 1A, mRNA (cDNA clone MGC:26821 IMAGE:4814750), complete cds.
AK095136 - Homo sapiens cDNA FLJ37817 fis, clone BRSSN2003820.
JD298514 - Sequence 279538 from Patent EP1572962.
JD527263 - Sequence 508287 from Patent EP1572962.
JD409849 - Sequence 390873 from Patent EP1572962.
JD065106 - Sequence 46130 from Patent EP1572962.
JD310418 - Sequence 291442 from Patent EP1572962.
JD278641 - Sequence 259665 from Patent EP1572962.
JD164440 - Sequence 145464 from Patent EP1572962.
JD097832 - Sequence 78856 from Patent EP1572962.
JD176725 - Sequence 157749 from Patent EP1572962.
JD075543 - Sequence 56567 from Patent EP1572962.
JD336206 - Sequence 317230 from Patent EP1572962.
JD472864 - Sequence 453888 from Patent EP1572962.
JD127640 - Sequence 108664 from Patent EP1572962.
JD444671 - Sequence 425695 from Patent EP1572962.
JD501470 - Sequence 482494 from Patent EP1572962.
JD511336 - Sequence 492360 from Patent EP1572962.
JD409058 - Sequence 390082 from Patent EP1572962.
JD300145 - Sequence 281169 from Patent EP1572962.
JD472924 - Sequence 453948 from Patent EP1572962.
JD126804 - Sequence 107828 from Patent EP1572962.
JD192317 - Sequence 173341 from Patent EP1572962.
JD193881 - Sequence 174905 from Patent EP1572962.
JD241315 - Sequence 222339 from Patent EP1572962.
JD089871 - Sequence 70895 from Patent EP1572962.
JD086821 - Sequence 67845 from Patent EP1572962.
JD278881 - Sequence 259905 from Patent EP1572962.
JD424608 - Sequence 405632 from Patent EP1572962.
AK127432 - Homo sapiens cDNA FLJ45524 fis, clone BRTHA2026290, highly similar to Homo sapiens RasGEF domain family, member 1A (RASGEF1A), mRNA.
JD405330 - Sequence 386354 from Patent EP1572962.
JD528972 - Sequence 509996 from Patent EP1572962.
KJ904024 - Synthetic construct Homo sapiens clone ccsbBroadEn_13418 RASGEF1A gene, encodes complete protein.
CU692692 - Synthetic construct Homo sapiens gateway clone IMAGE:100018263 5' read RASGEF1A mRNA.
JD079008 - Sequence 60032 from Patent EP1572962.
JD470138 - Sequence 451162 from Patent EP1572962.
JD351386 - Sequence 332410 from Patent EP1572962.
JD226931 - Sequence 207955 from Patent EP1572962.
JD173706 - Sequence 154730 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8N9B8 (Reactome details) participates in the following event(s):

R-HSA-5672965 RAS GEFs promote RAS nucleotide exchange
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-5683057 MAPK family signaling cascades
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000395810.1, ENST00000395810.2, ENST00000395810.3, ENST00000395810.4, ENST00000395810.5, NM_145313, Q8N9B8, Q8TBF1, RGF1A_HUMAN, uc001jap.1, uc001jap.2, uc001jap.3, uc001jap.4
UCSC ID: ENST00000395810.6
RefSeq Accession: NM_145313
Protein: Q8N9B8 (aka RGF1A_HUMAN)
CCDS: CCDS7202.2, CCDS60517.1

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