Human Gene ARHGEF5 (ENST00000056217.10_5) from GENCODE V47lift37
  Description: Rho guanine nucleotide exchange factor 5 (from RefSeq NM_005435.4)
Gencode Transcript: ENST00000056217.10_5
Gencode Gene: ENSG00000050327.15_14
Transcript (Including UTRs)
   Position: hg19 chr7:144,052,495-144,077,725 Size: 25,231 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr7:144,059,763-144,077,149 Size: 17,387 Coding Exon Count: 14 

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 (chr7:144,052,495-144,077,725)mRNA (may differ from genome)Protein (1597 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ARHG5_HUMAN
DESCRIPTION: RecName: Full=Rho guanine nucleotide exchange factor 5; AltName: Full=Ephexin-3; AltName: Full=Guanine nucleotide regulatory protein TIM; AltName: Full=Oncogene TIM; AltName: Full=Transforming immortalized mammary oncogene; AltName: Full=p60 TIM;
TISSUE SPECIFICITY: Mainly expressed in kidney, liver, pancreas, lung and placenta.
SIMILARITY: Contains 1 DH (DBL-homology) domain.
SIMILARITY: Contains 1 PH domain.
SIMILARITY: Contains 1 SH3 domain.
SEQUENCE CAUTION: Sequence=BAD18708.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  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: ARHGEF5
Diseases sorted by gene-association score: warsaw breakage syndrome (2)

-  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: 9.84 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 87.45 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 -48.50112-0.433 Picture PostScript Text
3' UTR -200.30576-0.348 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
IPR000219 - DH-domain
IPR001331 - GDS_CDC24_CS
IPR011993 - PH_like_dom
IPR001849 - Pleckstrin_homology
IPR001452 - SH3_domain

Pfam Domains:
PF00018 - SH3 domain
PF00621 - RhoGEF domain
PF07653 - Variant SH3 domain
PF14604 - Variant SH3 domain
PF15441 - RhoGEF 5/35 N-terminal disordered region

SCOP Domains:
48065 - DBL homology domain (DH-domain)
50044 - SH3-domain
50729 - PH domain-like

ModBase Predicted Comparative 3D Structure on Q12774
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:0005085 guanyl-nucleotide exchange factor activity
GO:0005089 Rho guanyl-nucleotide exchange factor activity
GO:0005515 protein binding
GO:0005525 GTP binding
GO:0008289 lipid binding

Biological Process:
GO:0002408 myeloid dendritic cell chemotaxis
GO:0007186 G-protein coupled receptor signaling pathway
GO:0030036 actin cytoskeleton organization
GO:0032956 regulation of actin cytoskeleton organization
GO:0035023 regulation of Rho protein signal transduction
GO:0035556 intracellular signal transduction
GO:0043065 positive regulation of apoptotic process
GO:0043087 regulation of GTPase activity
GO:0043507 positive regulation of JUN kinase activity
GO:0043547 positive regulation of GTPase activity
GO:0051056 regulation of small GTPase mediated signal transduction
GO:0051091 positive regulation of sequence-specific DNA binding transcription factor activity
GO:0051493 regulation of cytoskeleton organization
GO:0051496 positive regulation of stress fiber assembly
GO:0071803 positive regulation of podosome assembly
GO:1904591 positive regulation of protein import
GO:0070372 regulation of ERK1 and ERK2 cascade

Cellular Component:
GO:0002102 podosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0030054 cell junction
GO:0042995 cell projection
GO:0071944 cell periphery


-  Descriptions from all associated GenBank mRNAs
  LF207113 - JP 2014500723-A/14616: Polycomb-Associated Non-Coding RNAs.
LP896472 - Sequence 1336 from Patent EP3253886.
AK160365 - Homo sapiens mRNA for FLJ00261 protein.
LF213730 - JP 2014500723-A/21233: Polycomb-Associated Non-Coding RNAs.
CR749203 - Homo sapiens mRNA; cDNA DKFZp686N1969 (from clone DKFZp686N1969).
BC136661 - Homo sapiens Rho guanine nucleotide exchange factor (GEF) 5, mRNA (cDNA clone MGC:168274 IMAGE:9020651), complete cds.
AB384425 - Synthetic construct DNA, clone: pF1KSDF0261, Homo sapiens ARHGEF5 gene for Rho guanine nucleotide exchange factor 5, complete cds, without stop codon, in Flexi system.
JD023459 - Sequence 4483 from Patent EP1572962.
JD031999 - Sequence 13023 from Patent EP1572962.
JD027175 - Sequence 8199 from Patent EP1572962.
JD030152 - Sequence 11176 from Patent EP1572962.
AK123596 - Homo sapiens cDNA FLJ41602 fis, clone CTONG3000084, highly similar to PROBABLE GUANINE NUCLEOTIDE REGULATORY PROTEIN TIM.
BX649178 - Homo sapiens mRNA; cDNA DKFZp686O18190 (from clone DKFZp686O18190).
AK090570 - Homo sapiens cDNA FLJ33251 fis, clone ASTRO2005242, highly similar to Rho guanine nucleotide exchange factor 5.
AX746515 - Sequence 40 from Patent EP1308459.
BC010046 - Homo sapiens Rho guanine nucleotide exchange factor (GEF) 5, mRNA (cDNA clone IMAGE:3636857), complete cds.
BC011839 - Homo sapiens Rho guanine nucleotide exchange factor (GEF) 5, mRNA (cDNA clone IMAGE:3953394), complete cds.
BC014555 - Homo sapiens Rho guanine nucleotide exchange factor (GEF) 5, mRNA (cDNA clone IMAGE:3614104), complete cds.
U02082 - Human guanine nucleotide regulatory protein (tim1) mRNA, complete cds.
JD043922 - Sequence 24946 from Patent EP1572962.
JD487397 - Sequence 468421 from Patent EP1572962.
CU679587 - Synthetic construct Homo sapiens gateway clone IMAGE:100019762 5' read ARHGEF5 mRNA.
DQ896485 - Synthetic construct Homo sapiens clone IMAGE:100010945; FLH194751.01L; RZPDo839E0970D Rho guanine nucleotide exchange factor (GEF) 5 (ARHGEF5) gene, encodes complete protein.
DQ893512 - Synthetic construct clone IMAGE:100006142; FLH194755.01X; RZPDo839E0980D Rho guanine nucleotide exchange factor (GEF) 5 (ARHGEF5) gene, encodes complete protein.
DQ786285 - Homo sapiens clone HLS_IMAGE_451095 mRNA sequence.
JD250081 - Sequence 231105 from Patent EP1572962.
JD055713 - Sequence 36737 from Patent EP1572962.
JD333612 - Sequence 314636 from Patent EP1572962.
JD080280 - Sequence 61304 from Patent EP1572962.
JD083968 - Sequence 64992 from Patent EP1572962.
MA442690 - JP 2018138019-A/14616: Polycomb-Associated Non-Coding RNAs.
MA449307 - JP 2018138019-A/21233: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_rhoPathway - Rho cell motility signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein Q12774 (Reactome details) participates in the following event(s):

R-HSA-194913 GEFs activate Rho GTPase:GDP
R-HSA-419166 GEFs activate RhoA,B,C
R-HSA-205039 p75NTR indirectly activates RAC and Cdc42 via a guanyl-nucleotide exchange factor
R-HSA-194840 Rho GTPase cycle
R-HSA-416482 G alpha (12/13) signalling events
R-HSA-193648 NRAGE signals death through JNK
R-HSA-194315 Signaling by Rho GTPases
R-HSA-388396 GPCR downstream signalling
R-HSA-204998 Cell death signalling via NRAGE, NRIF and NADE
R-HSA-162582 Signal Transduction
R-HSA-372790 Signaling by GPCR
R-HSA-193704 p75 NTR receptor-mediated signalling
R-HSA-73887 Death Receptor Signalling

-  Other Names for This Gene
  Alternate Gene Symbols: A6NNJ2, ARHG5_HUMAN, ENST00000056217.1, ENST00000056217.2, ENST00000056217.3, ENST00000056217.4, ENST00000056217.5, ENST00000056217.6, ENST00000056217.7, ENST00000056217.8, ENST00000056217.9, NM_005435, Q12774, Q6ZML7, TIM, uc317caf.1, uc317caf.2
UCSC ID: ENST00000056217.10_5
RefSeq Accession: NM_005435.4
Protein: Q12774 (aka ARHG5_HUMAN or ARH5_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.