Ccdc42 (coiled-coil domain containing 42) - Rat Genome Database

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Gene: Ccdc42 (coiled-coil domain containing 42) Mus musculus
Analyze
Symbol: Ccdc42
Name: coiled-coil domain containing 42
RGD ID: 1623720
MGI Page MGI
Description: Involved in spermatid development. Acts upstream of or within acrosome assembly; centrosome cycle; and cilium assembly. Predicted to be located in ciliary base. Orthologous to human CCDC42 (coiled-coil domain containing 42).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: A530001H01Rik; coiled-coil domain-containing protein 42; coiled-coil domain-containing protein 42A
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391168,477,863 - 68,488,777 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1168,477,847 - 68,488,792 (+)EnsemblGRCm39 Ensembl
GRCm381168,587,037 - 68,597,951 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1168,587,021 - 68,597,966 (+)EnsemblGRCm38mm10GRCm38
MGSCv371168,400,539 - 68,411,453 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361168,410,250 - 68,414,149 (+)NCBIMGSCv36mm8
Celera1175,524,206 - 75,536,769 (+)NCBICelera
Cytogenetic Map11B3NCBI
cM Map1141.85NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:16141072   PMID:16141073   PMID:21267068   PMID:21873635   PMID:26945718   PMID:31475146  
PMID:32325033   PMID:34124066   PMID:35587122   PMID:38038747  


Genomics

Comparative Map Data
Ccdc42
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391168,477,863 - 68,488,777 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1168,477,847 - 68,488,792 (+)EnsemblGRCm39 Ensembl
GRCm381168,587,037 - 68,597,951 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1168,587,021 - 68,597,966 (+)EnsemblGRCm38mm10GRCm38
MGSCv371168,400,539 - 68,411,453 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361168,410,250 - 68,414,149 (+)NCBIMGSCv36mm8
Celera1175,524,206 - 75,536,769 (+)NCBICelera
Cytogenetic Map11B3NCBI
cM Map1141.85NCBI
CCDC42
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38178,729,935 - 8,744,836 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl178,729,935 - 8,745,219 (-)EnsemblGRCh38hg38GRCh38
GRCh37178,633,253 - 8,648,154 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36178,573,977 - 8,588,879 (-)NCBINCBI36Build 36hg18NCBI36
Celera178,664,029 - 8,678,936 (-)NCBICelera
Cytogenetic Map17p13.1NCBI
HuRef178,532,149 - 8,547,081 (-)NCBIHuRef
CHM1_1178,642,316 - 8,657,225 (-)NCBICHM1_1
T2T-CHM13v2.0178,636,013 - 8,650,898 (-)NCBIT2T-CHM13v2.0
Ccdc42
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81053,788,833 - 53,799,011 (+)NCBIGRCr8
mRatBN7.21053,289,956 - 53,300,135 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1053,289,956 - 53,300,135 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1057,949,747 - 57,959,920 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01057,438,785 - 57,448,960 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01052,947,793 - 52,957,965 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01055,169,312 - 55,179,489 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1055,169,282 - 55,181,416 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01054,913,271 - 54,923,448 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41055,339,083 - 55,349,260 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1052,458,268 - 52,468,446 (+)NCBICelera
Cytogenetic Map10q24NCBI
Ccdc42
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554678,207,590 - 8,224,423 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554678,207,590 - 8,220,426 (+)NCBIChiLan1.0ChiLan1.0
CCDC42
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21965,004,385 - 65,026,228 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11769,813,573 - 69,835,349 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01742,908,881 - 42,924,815 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11747,642,537 - 47,657,607 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1747,642,537 - 47,660,983 (+)Ensemblpanpan1.1panPan2
CCDC42
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1533,436,642 - 33,445,644 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl533,436,644 - 33,445,644 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha533,573,388 - 33,582,285 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0533,539,989 - 33,549,077 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl533,539,991 - 33,549,148 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1533,508,031 - 33,516,914 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0533,465,076 - 33,474,163 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0533,641,719 - 33,650,805 (-)NCBIUU_Cfam_GSD_1.0
Ccdc42
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560248,432,923 - 48,445,652 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365951,907,312 - 1,919,305 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365951,907,312 - 1,919,305 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC42
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1253,869,567 - 53,884,128 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11253,869,559 - 53,883,929 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21256,619,323 - 56,633,751 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC42
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1168,087,741 - 8,103,964 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl168,087,943 - 8,101,960 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605913,279,269 - 13,295,942 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc42
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478611,282,620 - 11,295,222 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478611,282,704 - 11,295,926 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc42
438 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:509
Count of miRNA genes:157
Interacting mature miRNAs:166
Transcripts:ENSMUST00000063006, ENSMUST00000102612, ENSMUST00000154294
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
26884453Sklq16_mskull length QTL 16, 16 week (mouse)11325000072690826Mouse
13208559Wght10_mweight 10 (mouse)11395000088890826Mouse
13208558Lgth12_mbody length 12 (mouse)11395000094890826Mouse
1300905Scc6_mcolon tumor susceptibility 6 (mouse)Not determined11688027789019734Mouse
26884401Huml4_mhumerus length 4, 10 week (mouse)111155000068490826Mouse
1357640Orq2_movulation rate QTL 2 (mouse)Not determined111226863768500330Mouse
4141127W3q4_mweight 3 weeks QTL 4 (mouse)Not determined1226863768500330Mouse
4141470Egq4_mearly growth QTL 4 (mouse)Not determined1226863768500330Mouse
4142109W10q2_mweight 10 weeks QTL 2 (mouse)Not determined1226863768500330Mouse
4141582Lgaq1_mlate growth adjusted QTL 1 (mouse)Not determined1226863768500330Mouse
4142308W6q3_mweight 6 weeks QTL 3 (mouse)Not determined111226863768500330Mouse
4142216Lgq1_mlate growth QTL 1 (mouse)Not determined1226863768500330Mouse
4141966Tailq1_mtail length QTL 1 (mouse)Not determined1226863768500330Mouse
1357851Scfq3_msubcutaneous fat pad weight QTL 3 (mouse)Not determined111226863768500330Mouse
1357720Kidpq1_mkidney weight percentage QTL 1 (mouse)Not determined111226863768500330Mouse
1357437Epfq4_mepididymal fat pad weight QTL 4 (mouse)Not determined111226863768500330Mouse
1559002Lmrq4_mLeishmania major resistance QTL 4 (mouse)Not determined111226863769684947Mouse
39128214Lwq20_mliver weight QTL 20 (mouse)1112268637118022724Mouse
10053687Eae6_msusceptibility to experimental allergic encephalomyelitis 6 (mouse)Not determined111778196668500330Mouse
4141894Nidd6k_mNidd6 on KK-A (mouse)Not determined1912420496897826Mouse
10412246Dfs2_mdental fluorosis suseptibility 2 (mouse)Not determined112180736495881231Mouse
1357782Char8_mP. chabaudi malaria resistance QTL 8 (mouse)Not determined113557861669684987Mouse
13208569Bmiq10_mbody mass index QTL 10 (mouse)113589082784890826Mouse
1301328Mol4_mmodifier of LPS-response 4 (mouse)Not determined113628257783481356Mouse
1301788Lbw8_mlupus NZB x NZW 8 (mouse)Not determined113650328770509492Mouse
1301896Tria1_mT-cell receptor induced activation 1 (mouse)Not determined113661356570613855Mouse
4141853Skmw17_mskeletal muscle weight 17 (mouse)Not determined113708094171081064Mouse
10766457Nwa3_mNew Zealand White autoimmunity 3 (mouse)113801611572016209Mouse
11532698Sluc36a_msusceptibility to lung cancer 36a (mouse)114225661776256730Mouse
11532699Sluc36b_msusceptibility to lung cancer 36b (mouse)114225661776256730Mouse
4142300Ctrq3_mC. trachomatis resistance QTL 3 (mouse)Not determined114463003876854757Mouse
4141367Inf1_macute ozone induced inflammation (mouse)Not determined44630038113058009Mouse
1302021Nidd1n_mnon-insulin-dependent diabetes mellitus 1 in NSY (mouse)Not determined114516587379978324Mouse
1357878Mastr_mmodifier of astrocytoma (mouse)Not determined114570858189818733Mouse
1300765Bbaa4_mB.burgdorferi-associated arthritis 4 (mouse)Not determined114618516780185262Mouse
1301988Bmd11_mbone mineral density 11 (mouse)Not determined114631940780319522Mouse
1301830Ssta4_msusceptibility to Salmonella typhimurium antigens 4 (mouse)Not determined115007819184078411Mouse
13524840Ppiq9a_mprepulse inhibition QTL 9a (mouse)115249438586494385Mouse
1300774Pgia7_mproteoglycan induced arthritis 7 (mouse)Not determined115339058887390737Mouse
4141830Pregq1_mpregnancy QTL 1 (mouse)Not determined115412675283733652Mouse
4141875Etax9_methanol induced ataxia 9 (mouse)Not determined5528498572209927Mouse
4142121Tmc1m2_mTmc1 modifier 2 (mouse)Not determined1156864027114157957Mouse
1300664Etohcta9_methanol conditioned taste aversion 9 (mouse)Not determined115775466091754758Mouse
10053682Eae45_mexperimental allergic encephalomyelitis susceptibility 45 (mouse)Not determined115849055574754758Mouse
1300924Ity2_mimmunity to S. typhimurium 2 (mouse)Not determined15850803087695238Mouse
4141982Skts-fp2_mskin tumor susceptibility in FVB and PWK 2 (mouse)Not determined5871926685066529Mouse
11532697Sluc36_msusceptibility to lung cancer 36 (mouse)115925661769482699Mouse
1301987Pid3_mprior incubation determinant 3 (mouse)Not determined116168682088699728Mouse
1301319Dautb4_mdopamine uptake transporter binding 4 (mouse)Not determined116215600596156153Mouse
27226730Tibmd1_mtibia midshaft diameter 1, 5 week (mouse)1162590826109390826Mouse
4141642Ltxs2_mlethal factor toxin susceptibility 2 (mouse)Not determined116304211368500330Mouse
1301999Lmr15_mleishmaniasis resistance 15 (mouse)Not determined116331940781830473Mouse
10044004Stzid3_mstreptozotocin induced diabetes susceptibility 3 (mouse)Not determined116331940794063918Mouse
11039502Ltpr6b_mLeishmania tropica response 6b (mouse)116483033698830473Mouse
11039501Ltpr6a_mLeishmania tropica response 6a (mouse)116483033698830473Mouse
11039515Ltpr6_mLeishmania tropica response 6 (mouse)116483033698830473Mouse
1357766Si5lq6_mserum IGFBP-5 level QTL 6 (mouse)Not determined1166733420100733652Mouse
1301546Pcir2_mperiosteal circumference 2 (mouse)Not determined1166733420100733652Mouse
1301833Tbbmd5_mtotal body bone mineral density 5 (mouse)Not determined1166733420100733652Mouse
1300628Lgth6_mbody length 6 (mouse)Not determined1166733420100733652Mouse
4141012Femwf6_mfemur work to failure 6 (mouse)Not determined66733420100733652Mouse
1300784Prdt3_mprion disease incubation time 3 (mouse)Not determined1166733420100733652Mouse
4142316Ity2b_mimmunity to S. typhimurium 2b (mouse)Not determined116707819179813912Mouse
27226783Tibl5_mtibia length 5, 5 week (mouse)1168190826101890826Mouse


Expression


Sequence


RefSeq Acc Id: ENSMUST00000063006   ⟹   ENSMUSP00000057342
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1168,477,959 - 68,488,771 (+)Ensembl
GRCm38.p6 Ensembl1168,587,133 - 68,597,945 (+)Ensembl
RefSeq Acc Id: ENSMUST00000102612   ⟹   ENSMUSP00000099672
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1168,484,881 - 68,488,780 (+)Ensembl
GRCm38.p6 Ensembl1168,594,055 - 68,597,954 (+)Ensembl
RefSeq Acc Id: ENSMUST00000154294   ⟹   ENSMUSP00000114381
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1168,477,847 - 68,488,792 (+)Ensembl
GRCm38.p6 Ensembl1168,587,021 - 68,597,966 (+)Ensembl
RefSeq Acc Id: NM_177779   ⟹   NP_808447
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391168,477,863 - 68,488,777 (+)NCBI
GRCm381168,587,037 - 68,597,951 (+)NCBI
MGSCv371168,400,539 - 68,411,453 (+)RGD
Celera1175,524,206 - 75,536,769 (+)RGD
cM Map11 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006533483   ⟹   XP_006533546
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391168,481,410 - 68,488,777 (+)NCBI
GRCm381168,590,575 - 68,597,951 (+)NCBI
Sequence:
RefSeq Acc Id: NP_808447   ⟸   NM_177779
- UniProtKB: B9EHU2 (UniProtKB/Swiss-Prot),   Q8BNY1 (UniProtKB/Swiss-Prot),   Q5SV66 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006533546   ⟸   XM_006533483
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSMUSP00000114381   ⟸   ENSMUST00000154294
RefSeq Acc Id: ENSMUSP00000057342   ⟸   ENSMUST00000063006
RefSeq Acc Id: ENSMUSP00000099672   ⟸   ENSMUST00000102612
Protein Domains
DUF4200

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5SV66-F1-model_v2 AlphaFold Q5SV66 1-316 view protein structure

Promoters
RGD ID:8675110
Promoter ID:EPDNEW_M15585
Type:initiation region
Name:Ccdc42_2
Description:Mus musculus coiled-coil domain containing 42 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M15586  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381168,587,000 - 68,587,060EPDNEW
RGD ID:8675112
Promoter ID:EPDNEW_M15586
Type:multiple initiation site
Name:Ccdc42_1
Description:Mus musculus coiled-coil domain containing 42 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M15585  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381168,593,992 - 68,594,052EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3045254 AgrOrtholog
Ensembl Genes ENSMUSG00000045915 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000063006.12 UniProtKB/TrEMBL
  ENSMUST00000102612.2 UniProtKB/Swiss-Prot
  ENSMUST00000154294 ENTREZGENE
  ENSMUST00000154294.8 UniProtKB/Swiss-Prot
InterPro DUF4200 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:3045254 ENTREZGENE
NCBI Gene 276920 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 42 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UNCHARACTERIZED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam DUF4200 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ccdc42 PhenoGen
UniProt B9EHU2 ENTREZGENE
  CCD42_MOUSE UniProtKB/Swiss-Prot
  Q5SV65_MOUSE UniProtKB/TrEMBL
  Q5SV66 ENTREZGENE
  Q8BNY1 ENTREZGENE
UniProt Secondary B9EHU2 UniProtKB/Swiss-Prot
  Q8BNY1 UniProtKB/Swiss-Prot