Human Gene CDC42EP4 (uc002jjn.3)
  Description: Homo sapiens CDC42 effector protein (Rho GTPase binding) 4 (CDC42EP4), mRNA.
RefSeq Summary (NM_012121): The product of this gene is a member of the CDC42-binding protein family. Members of this family interact with Rho family GTPases and regulate the organization of the actin cytoskeleton. This protein has been shown to bind both CDC42 and TC10 GTPases in a GTP-dependent manner. When overexpressed in fibroblasts, this protein was able to induce pseudopodia formation, which suggested a role in inducing actin filament assembly and cell shape control. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr17:71,279,763-71,307,054 Size: 27,292 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr17:71,281,569-71,282,639 Size: 1,071 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:71,279,763-71,307,054)mRNA (may differ from genome)Protein (356 aa)
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OMIMPubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: BORG4_HUMAN
DESCRIPTION: RecName: Full=Cdc42 effector protein 4; AltName: Full=Binder of Rho GTPases 4;
FUNCTION: Probably involved in the organization of the actin cytoskeleton. May act downstream of CDC42 to induce actin filament assembly leading to cell shape changes. Induces pseudopodia formation, when overexpressed in fibroblasts.
SUBUNIT: Interacts with CDC42 and RHOQ, in a GTP-dependent manner (By similarity).
SUBCELLULAR LOCATION: Endomembrane system; Peripheral membrane protein. Cytoplasm, cytoskeleton.
TISSUE SPECIFICITY: Not detected in any of the adult tissues tested. May be expressed only in fetal or embryonic tissues.
SIMILARITY: Belongs to the BORG/CEP family.
SIMILARITY: Contains 1 CRIB 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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 39.79 RPKM in Brain - Cerebellum
Total median expression: 1036.74 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 -45.10147-0.307 Picture PostScript Text
3' UTR -675.671806-0.374 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
IPR000095 - PAK_box_Rho-bd

Pfam Domains:
PF00786 - P21-Rho-binding domain
PF14957 - Cdc42 effector

ModBase Predicted Comparative 3D Structure on Q9H3Q1
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     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005096 GTPase activator activity
GO:0005515 protein binding
GO:0017049 GTP-Rho binding

Biological Process:
GO:0007266 Rho protein signal transduction
GO:0008360 regulation of cell shape
GO:0030838 positive regulation of actin filament polymerization
GO:0031274 positive regulation of pseudopodium assembly
GO:0043547 positive regulation of GTPase activity
GO:0071346 cellular response to interferon-gamma

Cellular Component:
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005913 cell-cell adherens junction
GO:0012505 endomembrane system
GO:0015629 actin cytoskeleton
GO:0015630 microtubule cytoskeleton
GO:0016020 membrane
GO:0045335 phagocytic vesicle


-  Descriptions from all associated GenBank mRNAs
  AB042237 - Homo sapiens Borg4 mRNA, complete cds.
BC002774 - Homo sapiens CDC42 effector protein (Rho GTPase binding) 4, mRNA (cDNA clone MGC:3740 IMAGE:3617435), complete cds.
AK097835 - Homo sapiens cDNA FLJ40516 fis, clone TESTI2046569, highly similar to Cdc42 effector protein 4 (Binder of RhoGTPases 4).
AK027385 - Homo sapiens cDNA FLJ14479 fis, clone MAMMA1002143, highly similar to Cdc42 effector protein 4 (Binder of Rho GTPases 4).
BC010451 - Homo sapiens CDC42 effector protein (Rho GTPase binding) 4, mRNA (cDNA clone MGC:17125 IMAGE:4181539), complete cds.
AK312536 - Homo sapiens cDNA, FLJ92905, Homo sapiens CDC42 effector protein (Rho GTPase binding) 4(CDC42EP4), mRNA.
AL162074 - Homo sapiens mRNA; cDNA DKFZp762L106 (from clone DKFZp762L106).
JD193619 - Sequence 174643 from Patent EP1572962.
JD133949 - Sequence 114973 from Patent EP1572962.
JD143181 - Sequence 124205 from Patent EP1572962.
JD291182 - Sequence 272206 from Patent EP1572962.
JD536346 - Sequence 517370 from Patent EP1572962.
JD306043 - Sequence 287067 from Patent EP1572962.
JD369724 - Sequence 350748 from Patent EP1572962.
JD519404 - Sequence 500428 from Patent EP1572962.
JD233484 - Sequence 214508 from Patent EP1572962.
JD043543 - Sequence 24567 from Patent EP1572962.
JD457884 - Sequence 438908 from Patent EP1572962.
JD426059 - Sequence 407083 from Patent EP1572962.
JD300302 - Sequence 281326 from Patent EP1572962.
JD415710 - Sequence 396734 from Patent EP1572962.
JD335219 - Sequence 316243 from Patent EP1572962.
JD541427 - Sequence 522451 from Patent EP1572962.
JD253854 - Sequence 234878 from Patent EP1572962.
JD437440 - Sequence 418464 from Patent EP1572962.
JD469813 - Sequence 450837 from Patent EP1572962.
JD536954 - Sequence 517978 from Patent EP1572962.
JD104108 - Sequence 85132 from Patent EP1572962.
JD108950 - Sequence 89974 from Patent EP1572962.
AF099664 - Homo sapiens Cdc42 effector protein 4 mRNA, complete cds.
HQ447559 - Synthetic construct Homo sapiens clone IMAGE:100070900; CCSB014690_01 CDC42 effector protein (Rho GTPase binding) 4 (CDC42EP4) gene, encodes complete protein.
KJ893406 - Synthetic construct Homo sapiens clone ccsbBroadEn_02800 CDC42EP4 gene, encodes complete protein.
KJ898515 - Synthetic construct Homo sapiens clone ccsbBroadEn_07909 CDC42EP4 gene, encodes complete protein.
AB463476 - Synthetic construct DNA, clone: pF1KB4182, Homo sapiens CDC42EP4 gene for CDC42 effector protein (Rho GTPase binding) 4, without stop codon, in Flexi system.
CU678188 - Synthetic construct Homo sapiens gateway clone IMAGE:100023072 5' read CDC42EP4 mRNA.
JD250532 - Sequence 231556 from Patent EP1572962.
JD510936 - Sequence 491960 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AB042237, BORG4, BORG4_HUMAN, CEP4, NM_012121, NP_036253, O95828, Q96FT3, Q9H3Q1
UCSC ID: uc002jjn.3
RefSeq Accession: NM_012121
Protein: Q9H3Q1 (aka BORG4_HUMAN or BOR4_HUMAN)
CCDS: CCDS11695.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AB042237.1
exon count: 2CDS single in 3' UTR: no RNA size: 2732
ORF size: 1071CDS single in intron: no Alignment % ID: 99.67
txCdsPredict score: 2315.00frame shift in genome: no % Coverage: 99.34
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 2709# 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.