Homo sapiens gene CDC42EP5, encoding CDC42 effector protein (Rho GTPase binding) 5.
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SUMMARY back to top
RefSeq summary
[CDC42EP5] CDC42, a small Rho GTPase, regulates the formation of F-actin-containing structures through its interaction with the downstream effector proteins. The protein encoded by this gene is a member of the Borg family of CDC42 effector proteins. Borg family proteins contain a CRIB (Cdc42/Rac interactive-binding) domain. They bind to, and negatively regulate the function of, CDC42. The specific function of this protein has not yet been determined. [provided by RefSeq].

RefSeq annotates one representative transcript (NM included in AceView variant.c), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 3 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 1.0 times the average gene in this release. The sequence of this gene is defined by 115 GenBank accessions from 93 cDNA clones, some from colon (seen 18 times), stomach (15), lung (11), colon tumor, RER+ (9), colonic mucosa from 3 patients with crohn'sdisease (6), pancreas (6), pooled human melanocyte, fetal heart, andpregnant uterus (6) and 36 other tissues. We annotate structural defects or features in 7 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 2 distinct gt-ag introns. Transcription produces 4 different mRNAs, 3 alternatively spliced variants and 1 unspliced form. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 3 validated alternative polyadenylation sites (see the diagram).
Function: There are 3 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in processes (positive regulation of actin filament polymerization, positive regulation of pseudopodium assembly, regulation of cell shape, JNK cascade, Rho protein signal transduction). Proteins are expected to have molecular functions (GTP-Rho binding, protein binding) and to localize in various compartments (cytoplasm, membrane, nucleus, cytoskeleton, endomembrane system, plasma membrane). Putative protein interactors have been described (CDC42, HSPC157ANDCDC42, SEPT7).
Protein coding potential: 2 spliced and the unspliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), some containing P21-Rho-binding domain [Pfam], apparently vertebrate specific. The remaining mRNA variant (spliced) appears not to encode a good protein. Finally proteins from this gene may be modulated by acetylation; mono-methylation; phosphorylation, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 19, links to other databases and other names
Map: This gene CDC42EP5 maps on chromosome 19, at 19q13.42 according to Entrez Gene. In AceView, it covers 8.23 kb, from 54984436 to 54976203 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 148170, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as CDC42EP5, XXbac-BCX535A19.5, CEP5, Borg3, MGC21945 or MGC71153, LOC148170. It has been described as cdc42 effector protein 5, 1700027J19Rik, 2010007O02Rik, binder of Rho GTPases 3, binder of Rho GTPase 3-like.
Closest AceView homologs in other species ?
The closest mouse genes, according to BlastP, are the AceView genes Cdc42ep5andLeng9 (e=10-31), mohite (e=10-31).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene ark-1 (e=0.006), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
CDC42EP5 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 0.68 1.78 0.78 6.65 1.35 6.65 0.83 24.8 3.57 4.10 0.96 20.2 14.3 1.35 2.70 3.57 3.57 2.05 0.83 0.78 0.63 1.18 0.51 17.6 1.78 1.35 0.72 3.10 1.02 7.13 0.59 0.42 2.90 1.91 1.55 0.59 1.66 5.79 0.32 0.48 2.70 4.39 0.59 5.40 0.78 0.32 1.78 4.71 1.26 1.45 0.96 0.89 1.55 1.26 46.3 1.91 0.36 3.10 1.78 0.42 0.36 0.68 0.68 1.91 23.2 2.35 0.48 0.96 40.3 1.91 2.19 0.83 5.04 1.91 0.78 2.05 1.45 18.8 1.66 0.89 1.78 0.51 0.96 0.89 1.18 12.4 0.96 3.33 2.19 4.10 0.48 0.48 0.96 1.45 1.45 26.6 1.02 1.26 0.48 2.35 1.18 1.66 2.52 46.3 0.48 0.39 2.70 1.91 0.45 5.79 0.24 0.48 0.59 2.52 0.36 0.96 1.02 0.59 2.70 1.45 1.10 0.36 0.59 6.65 1.02 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene CDC42EP5 5' 3' encoded on minus strand of chromosome 19 from 54,984,436 to 54,976,203 23306 b a-u 23306 12410 c [NM] 12410 d 500bp 0 226 bp exon 226 bp exon 1304 bp [gt-ag] intron 40 GenBank accessions 23266 RNA-seq supporting reads 1926 UHR pooled cells 551 Brain 3 Blood 20486 Neuroblastoma 300 Other (also 4402 Primates bodymap) 231 bp exon 2 accessions, some from ovary (seen once) prostate (once) capped 5' end, 1 accession 231 bp exon 749 bp exon 749 bp exon 93 bp uORF 749 bp exon 749 bp exon 53 accessions, some from colon (seen 15 times) colon tumor, RER+ (6) colonic mucosa from 3 patients with crohn'sdisease (6) pooled human melanocyte fetal heart, andpregnant uterus (6) lung (4) Validated 3' end, 19 accessions 749 bp exon 212 bp exon 1304 bp [gt-ag] intron 40 GenBank accessions 23266 RNA-seq supporting reads 1926 UHR pooled cells 551 Brain 3 Blood 20486 Neuroblastoma 300 Other (also 4402 Primates bodymap) 141 bp exon 6034 bp [gt-ag] intron 50 GenBank accessions 12360 RNA-seq supporting reads 952 UHR pooled cells 496 Brain 18 Blood 10754 Neuroblastoma 140 Other (also 664 Primates bodymap) 522 bp exon 37 accessions, NM_145057.2 some from stomach (seen 13 times) lung (5), cell lines (2) chondrosarcoma lung metastasis cell lines (2) enchondroma (2) Validated 3' end, 16 accessions 522 bp exon 159 bp exon 6034 bp [gt-ag] intron 50 GenBank accessions 12360 RNA-seq supporting reads 952 UHR pooled cells 496 Brain 18 Blood 10754 Neuroblastoma 140 Other (also 664 Primates bodymap) 522 bp exon 11 accessions, some from islets of langerhans (seen 4 times) pancreas (4), lung (2) ascites (once), eye (once) Validated 3' end, 6 accessions 522 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10-unspliced 749 bp 148 aa 226 bp 76 bp 90 bp 2kb possibly including promoter 749 bp 1kb
bAug10 457 bp 89 aa 184 bp 2kb including Promoter 1761 bp 1kb
cAug10 875 bp 148 aa 353 bp 75 bp 2kb probably including promoter 8213 bp 1kb
dAug10 681 bp 148 aa 159 bp 75 bp 2kb possibly including promoter 6715 bp 1kb

Gene neighbors and Navigator on chromosome 19q13.42 back to top
C R P NDUFA3 C R P PRPF31 D C I R P CNOT3 C I R P TSEN34 D C I R P RPS9 C I R P C TTYH1 C R P LENG8 C I R P LAIR2 C R P KIR3DX1 C R P LILRA2andLILRA1andLILRB1 C I R P VN1R105PandLILRB4 D C I R P LILRP1 P LILRP2 C P KIR3DL3 D C P KIR2DL3 D C I R P KIR2D_ D C I R P KIR3DP1andKIR2DL4 D C I R P FCAR D C I R P NCR1 D C I R P NLRP2andRPL36AP50 C R P VSTM1 D C R P TARM1 D C I R P OSCAR C I R P TFPT R C I R P LENG1 C R P TMC4 D C R P MBOAT7 C R P LILRA6andLILRB3 C R P LILRB5 D C I R P LILRB2 D C I R P LILRA3 C R P LILRA4andVN1R104PandLILRA5 D C I R P LAIR1 R R C R C P LENG9 C I R P CDC42EP5 R C D C R P NLRP7 100kb 0 CACNG8, 4 accessions CACNG6, 15 accessions 4 variants NDUFA3, 235 accessions 20 variants PRPF31, 269 accessions 13 variants CNOT3, 355 accessions 15 variants TSEN34, 359 accessions 6 variants RPS9, 598 accessions, 22 variants ruyuro, 2 accessions, 2 variants TTYH1, 314 accessions 23 variants LENG8, 508 accessions 12 variants LAIR2, 24 accessions, 5 variants KIR3DX1, 36 accessions 7 variants LILRA2andLILRA1andLILRB1 279 accessions, 32 variants VN1R105PandLILRB4, 174 accessions 14 variants LILRP1, 1 accession LILRP2, 4 accessions, 2 variants KIR3DL3, 21 accessions KIR2DL3, 34 accessions 2 variants KIR2D_, 182 accessions 13 variants KIR3DP1andKIR2DL4, 39 accessions 9 variants FCAR, 72 accessions, 15 variants NCR1, 33 accessions, 11 variants sparblu, 1 accession spawblu, 2 accessions vytabu, 15 accessions turaru, 40 accessions 2 variants sorwoy, 1 accession steeka, 1 accession vortabu, 3 accessions verwoy, 1 accession wernee, 2 accessions swaka, 1 accession shawwoy, 1 accession watabu, 2 accessions swawka, 1 accession boky, 1 accession klaber, 1 accession jeeblo, 1 accession wutabu, 4 accessions lablo, 12 accessions lyblo, 1 accession bawky, 1 accession deyky, 1 accession nublo, 1 accession smywoy, 1 accession keruri, 1 accession klyber, 1 accession fuky, 1 accession fawky, 2 accessions snuwoy, 1 accession zytabu, 1 accession sporwa, 1 accession speywa, 1 accession dawza, 1 accession toblo, 1 accession smarnee, 3 accessions forky, 2 accessions smoynee, 2 accessions zawtabu, 1 accession vawblo, 1 accession verblo, 2 accessions woyblo, 1 accession zablo, 1 accession zarblo, 3 accessions snoynee, 1 accession zertabu, 1 accession zawblo, 3 accessions wareri, 1 accession zeyblo, 1 accession zeytabu, 2 accessions zorblo, 1 accession heyuro, 1 accession zoytabu, 1 accession bleenee, 1 accession chawtabu, 1 accession juza, 1 accession blyblo, 6 accessions jawza, 1 accession karky, 1 accession vatabu, 1 accession swablu, 1 accession veytabu, 1 accession steyka, 1 accession slysarbo, 2 accessions bublo, 2 accessions vawoy, 2 accessions wynee, 2 accessions cheywoy, 1 accession florser, 1 accession doblo, 1 accession klywoy, 1 accession swoka, 1 accession feyblo, 1 accession klawwoy, 1 accession skarwoy, 1 accession slowoy, 1 accession jorblo, 10 accessions sleewoy, 1 accession koblo, 2 accessions blanee, 1 accession mablo, 1 accession moblo, 1 accession meyblo, 1 accession doyky, 1 accession nyblo, 1 accession neyblo, 1 accession foky, 1 accession wortabu, 1 accession dusor, 13 accessions reeblo, 1 accession rerblo, 1 accession sorblo, 2 accessions duza, 1 accession slynee, 3 accessions feeky, 1 accession deysor, 14 accessions torseebu, 2 accessions vyblo, 8 accessions voblo, 1 accession wawblo, 2 accessions zortabu, 1 accession chatabu, 2 accessions choblo, 1 accession chutabu, 1 accession gyky, 1 accession VSTM1, 34 accessions, 7 variants TARM1, 6 accessions, 2 variants OSCAR, 86 accessions, 10 variants TFPT, 180 accessions, 8 variants borblo, 1 accession LENG1, 35 accessions TMC4, 136 accessions, 12 variants MBOAT7, 573 accessions 14 variants LILRA6andLILRB3, 207 accessions 27 variants LILRB5, 190 accessions 16 variants LILRB2, 149 accessions 13 variants LILRA3, 38 accessions 2 variants LILRA4andVN1R104PandLILRA5 50 accessions, 10 variants LAIR1, 304 accessions 37 variants deesor, 2 accessions swutee, 1 accession zotabu, 3 accessions jysarbo, 6 accessions 3 variants LENG9, 1 accession CDC42EP5, 110 accessions 4 variants sikera, 2 accessions geeky, 2 accessions NLRP7, 65 accessions, 6 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               3 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a-u, .b, .c, .d Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes CI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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