Human Gene ARHGEF38 (uc003hxv.2) Description and Page Index
  Description: Homo sapiens Rho guanine nucleotide exchange factor (GEF) 38 (ARHGEF38), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr4:106,473,777-106,602,070 Size: 128,294 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr4:106,473,923-106,599,094 Size: 125,172 Coding Exon Count: 14 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:106,473,777-106,602,070)mRNA (may differ from genome)Protein (777 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsH-INV
HGNCLynxMGIPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: C9JIB4_HUMAN
DESCRIPTION: SubName: Full=Rho guanine nucleotide exchange factor 38;
SIMILARITY: Contains 2 SH3 domains.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ARHGEF38
CDC HuGE Published Literature: ARHGEF38
Positive Disease Associations: Echocardiography , Hypertension , Triglycerides
Related Studies:
  1. Echocardiography
    Ramachandran S Vasan et al. BMC medical genetics 2007, Genome-wide association of echocardiographic dimensions, brachial artery endothelial function and treadmill exercise responses in the Framingham Heart Study., BMC medical genetics. [PubMed 17903301]
    In hypothesis-generating GWAS of echocardiography, ETT and BA vascular function in a moderate-sized community-based sample, we identified several SNPs that are candidates for replication attempts and we provide a web-based GWAS resource for the research community.
  2. Hypertension
    , , . [PubMed 0]
  3. Hypertension
    , , . [PubMed 0]
           more ... click here to view the complete list

-  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: 3.15 RPKM in Minor Salivary Gland
Total median expression: 21.19 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 -38.90146-0.266 Picture PostScript Text
3' UTR -683.422976-0.230 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
IPR004148 - BAR_dom
IPR000219 - DH-domain
IPR011511 - SH3_2
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF00621 - RhoGEF domain
PF07653 - Variant SH3 domain
PF14604 - Variant SH3 domain

SCOP Domains:
48065 - DBL homology domain (DH-domain)
50044 - SH3-domain

ModBase Predicted Comparative 3D Structure on C9JIB4
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 orthologGenome BrowserNo orthologNo orthologNo ortholog
      
      
  Ensembl   
  Protein Sequence   
  Alignment   

-  Descriptions from all associated GenBank mRNAs
  AK000191 - Homo sapiens cDNA FLJ20184 fis, clone COLF0287.
BC105695 - Homo sapiens hypothetical protein FLJ20184, mRNA (cDNA clone MGC:125524 IMAGE:40023595), complete cds.
JD074572 - Sequence 55596 from Patent EP1572962.
JD137316 - Sequence 118340 from Patent EP1572962.
JD113823 - Sequence 94847 from Patent EP1572962.
KJ894073 - Synthetic construct Homo sapiens clone ccsbBroadEn_03467 ARHGEF38 gene, encodes complete protein.
AK125951 - Homo sapiens cDNA FLJ43963 fis, clone TESTI4016882.

-  Other Names for This Gene
  Alternate Gene Symbols: C9JIB4, C9JIB4_HUMAN, NM_001242729, NP_001229658
UCSC ID: uc003hxv.2
RefSeq Accession: NM_001242729
Protein: C9JIB4 CCDS: CCDS56338.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001242729.1
exon count: 14CDS single in 3' UTR: no RNA size: 5456
ORF size: 2334CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 4868.00frame shift in genome: no % Coverage: 100.00
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.