Human Gene RALGPS1 (uc011mab.2)
  Description: Homo sapiens Ral GEF with PH domain and SH3 binding motif 1 (RALGPS1), transcript variant 4, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:129,677,053-129,946,603 Size: 269,551 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr9:129,724,569-129,946,390 Size: 221,822 Coding Exon Count: 11 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:129,677,053-129,946,603)mRNA (may differ from genome)Protein (384 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMGIOMIMPubMedTreefam
UniProtKBBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RALGPS1
CDC HuGE Published Literature: RALGPS1
Positive Disease Associations: Body Mass Index
Related Studies:
  1. Body Mass Index
    , , . [PubMed 0]

-  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: 15.18 RPKM in Brain - Cerebellum
Total median expression: 176.91 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -170.40304-0.561 Picture PostScript Text
3' UTR -86.00213-0.404 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
  Pfam Domains:
PF00617 - RasGEF domain

SCOP Domains:
48366 - Ras GEF

ModBase Predicted Comparative 3D Structure on Q5JS13-3
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 Details     
Gene Sorter     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AB002349 - Homo sapiens mRNA for KIAA0351 gene.
BC033708 - Homo sapiens Ral GEF with PH domain and SH3 binding motif 1, mRNA (cDNA clone MGC:45125 IMAGE:3901593), complete cds.
AK299149 - Homo sapiens cDNA FLJ61342 complete cds, highly similar to Homo sapiens Ral GEF with PH domain and SH3 binding motif 1 (RALGPS1), mRNA.
BC032372 - Homo sapiens Ral GEF with PH domain and SH3 binding motif 1, mRNA (cDNA clone MGC:40302 IMAGE:5163332), complete cds.
AF221098 - Homo sapiens Ral guanine nucleotide exchange factor RalGPS1A mRNA, complete cds.
CU689706 - Synthetic construct Homo sapiens gateway clone IMAGE:100018190 5' read RALGPS1 mRNA.
AB385313 - Synthetic construct DNA, clone: pF1KA0351, Homo sapiens RALGPS1 gene for ral GEF with PH domain and SH3 binding motif 1, complete cds, without stop codon, in Flexi system.
BX648170 - Homo sapiens mRNA; cDNA DKFZp686K169 (from clone DKFZp686K169).
JD158026 - Sequence 139050 from Patent EP1572962.
BC019329 - Homo sapiens Ral GEF with PH domain and SH3 binding motif 1, mRNA (cDNA clone IMAGE:3503102), partial cds.
JD216856 - Sequence 197880 from Patent EP1572962.
JD382190 - Sequence 363214 from Patent EP1572962.
JD338062 - Sequence 319086 from Patent EP1572962.
JD167569 - Sequence 148593 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BC033708, KIAA0351, NM_001190730, NP_001177659, Q5JS13-3, RALGEF2
UCSC ID: uc011mab.2
RefSeq Accession: NM_001190730
Protein: Q5JS13-3, splice isoform of Q5JS13

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC033708.1
exon count: 12CDS single in 3' UTR: no RNA size: 1678
ORF size: 1155CDS single in intron: no Alignment % ID: 99.76
txCdsPredict score: 2211.00frame shift in genome: no % Coverage: 98.57
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.