Ccdc78 (coiled-coil domain containing 78) - Rat Genome Database

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Gene: Ccdc78 (coiled-coil domain containing 78) Mus musculus
Analyze
Symbol: Ccdc78
Name: coiled-coil domain containing 78
RGD ID: 1622805
MGI Page MGI
Description: Predicted to be involved in de novo centriole assembly involved in multi-ciliated epithelial cell differentiation and skeletal muscle contraction. Located in cytoplasm. Human ortholog(s) of this gene implicated in centronuclear myopathy 4. Orthologous to human CCDC78 (coiled-coil domain containing 78).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: coiled-coil domain-containing protein 78; Gm938; Gm950
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391726,005,554 - 26,009,487 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1726,005,554 - 26,009,487 (+)EnsemblGRCm39 Ensembl
GRCm381725,786,580 - 25,790,513 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1725,786,580 - 25,790,513 (+)EnsemblGRCm38mm10GRCm38
MGSCv371725,923,525 - 25,927,458 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361725,514,180 - 25,518,113 (+)NCBIMGSCv36mm8
Celera1726,319,386 - 26,323,319 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1712.89NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
centriole  (ISO,ISS)
cytoplasm  (IBA,IDA)
deuterosome  (ISO,ISS)
perinuclear region of cytoplasm  (ISO,ISS)
sarcolemma  (ISO,ISS)
sarcoplasmic reticulum  (ISO,ISS)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:16141072   PMID:16141073   PMID:18799693   PMID:20577004   PMID:21267068   PMID:21873635  
PMID:38355793  


Genomics

Comparative Map Data
Ccdc78
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391726,005,554 - 26,009,487 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1726,005,554 - 26,009,487 (+)EnsemblGRCm39 Ensembl
GRCm381725,786,580 - 25,790,513 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1725,786,580 - 25,790,513 (+)EnsemblGRCm38mm10GRCm38
MGSCv371725,923,525 - 25,927,458 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361725,514,180 - 25,518,113 (+)NCBIMGSCv36mm8
Celera1726,319,386 - 26,323,319 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1712.89NCBI
CCDC78
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3816722,582 - 726,880 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl16722,582 - 726,954 (-)EnsemblGRCh38hg38GRCh38
GRCh3716772,582 - 776,880 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3616712,583 - 716,460 (-)NCBINCBI36Build 36hg18NCBI36
Celera16972,747 - 976,638 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef16694,483 - 698,374 (-)NCBIHuRef
CHM1_116772,552 - 776,443 (-)NCBICHM1_1
T2T-CHM13v2.016726,756 - 731,054 (-)NCBIT2T-CHM13v2.0
Ccdc78
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81015,312,403 - 15,316,800 (+)NCBIGRCr8
mRatBN7.21014,808,355 - 14,812,284 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,807,710 - 14,812,282 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01015,155,839 - 15,160,039 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,156,207 - 15,159,894 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01014,969,092 - 14,972,982 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41015,052,949 - 15,064,350 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1014,477,059 - 14,481,260 (+)NCBICelera
Cytogenetic Map10q12NCBI
Ccdc78
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544216,478,795 - 16,482,263 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544216,478,219 - 16,482,452 (+)NCBIChiLan1.0ChiLan1.0
CCDC78
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v218963,198 - 967,657 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1164,747,036 - 4,751,251 (-)NCBINHGRI_mPanPan1
PanPan1.116735,786 - 740,155 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl16735,974 - 739,572 (-)Ensemblpanpan1.1panPan2
CCDC78
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1639,857,182 - 39,861,437 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl639,857,304 - 39,875,418 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha641,121,770 - 41,126,722 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0640,200,243 - 40,205,198 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl640,200,450 - 40,204,561 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1639,888,852 - 39,893,802 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0639,849,066 - 39,854,010 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0640,327,941 - 40,332,894 (+)NCBIUU_Cfam_GSD_1.0
Ccdc78
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344112,192,468 - 112,196,469 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936501289,765 - 294,272 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC78
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl341,053,936 - 41,057,734 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1341,053,926 - 41,057,735 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2341,420,178 - 41,424,583 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC78
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.15642,500 - 646,337 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606830,489,336 - 30,493,389 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc78
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249131,531,511 - 1,535,067 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249131,531,325 - 1,535,637 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc78
143 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:157
Count of miRNA genes:143
Interacting mature miRNAs:151
Transcripts:ENSMUST00000095500
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
1558807Ceat1_mchronic experimental autoimmune thyroiditis 1 (mouse)Not determined171263668226401133Mouse
12910528Nrq1_mnoise-induced hearing loss resistant QTL 1 (mouse)17129198453Mouse
1302038Radpf1_mradiation pulmonary fibrosis 1 (mouse)Not determined171683545533819843Mouse
1300890Bhr3_mbronchial hyperresponsiveness 3 (mouse)Not determined17397489048866091Mouse
1300995Fembrs4_mfemur breaking strength 4 (mouse)Not determined171506165249061760Mouse
1300613Pcyts4_mplasmacytoma susceptibility 4 (mouse)Not determined17127081639Mouse
4141608Phl1_mprogressive hearing loss 1 (mouse)Not determined17787584329487423Mouse
1302152Skull25_mskull morphology 25 (mouse)Not determined171681972150819843Mouse
1302028Asbb3_mautoimmune susceptibility in C57BL/6J and BALB/c 3 (mouse)Not determined171087811944878219Mouse
15039354Nmrs36_mNAFLD-associated magnetic resonance shift 36 (mouse)171914502553145025Mouse
4141215Mnic1_mmacronutrient intake, carbohydrate 1 (mouse)Not determined485475245670266Mouse
1300787Cd8mts5_mCD8 memory T cell subset 5 (mouse)Not determined17858491442585149Mouse
13524847Asrq8a_macoustic startle response 8a (mouse)171264696146646961Mouse
1300914Pcir4_mperiosteal circumference 4 (mouse)Not determined171506165249061760Mouse
13452396Leusq3_mleucocytosis susceptibility QTL 3 (mouse)171746220851462345Mouse
13452399Leusq6_mleucocytosis susceptibility QTL 6 (mouse)171746220851462345Mouse
1300535Char3_mP. chabaudi malaria resistance QTL 3 (mouse)Not determined171746220851462345Mouse
1302070Tbbmd7_mtotal body bone mineral density 7 (mouse)Not determined171506165249061760Mouse
10412214Sxbq3_mSGC/Knj cross B6 QTL 3 (mouse)Not determined171746220851462345Mouse
10412083Sm2_msusceptibility to Schistosoma mansoni infection 2 (mouse)Not determined171702994351030078Mouse
10043949Pbft7_mpercent body fat 7 (mouse)Not determined17689393640893936Mouse
4141067Hbnr2_mHeligmosomoides bakeri nematode resistance 2 (mouse)Not determined1188597145886119Mouse
12904946Tammq8_mtibialis anterior muscle mass QTL 8 (mouse)171245178746451787Mouse
10412198Sst5_msusceptibility to tuberculosis 5 (mouse)Not determined172507658355712970Mouse
4142342Lfnq4_mlung function QTL 4 (mouse)Not determined1120648439364059Mouse
10412196Bbaa28_mB.burgdorferi-associated arthritis 28 (mouse)Not determined172558491443976235Mouse
1357743Lith3_mlithogenic gene 3 (mouse)Not determined17126194456Mouse
1301935Skull24_mskull morphology 24 (mouse)Not determined17858491442585149Mouse
13524851Asrq8_macoustic startle response 8 (mouse)17131030170Mouse
1301331Lbw1_mlupus NZB x NZW 1 (mouse)Not determined171841835752420983Mouse
12910982Pifs2_mpeptide-induced fatal syndrome 2 (mouse)17126189355Mouse
1301840Ssial4_msusceptibility to sialadenitiss 4 (mouse)Not determined171817541252178214Mouse
1302100Circp2_mcircadian photosensitivity 2 (mouse)Not determined17129198453Mouse
1357789Kdnw3_mkidney weight 3 (mouse)Not determined17485475247885665Mouse
1301338Lmr1_mleishmaniasis resistance 1 (mouse)Not determined171008134086996400Mouse
1301056Pas2_mpulmonary adenoma susceptibility 2 (mouse)Not determined171842214152424327Mouse
1301327Lmr7_mleishmaniasis resistance 7 (mouse)Not determined17485475227715939Mouse
1301454Eae5_msusceptibility to experimental allergic encephalomyelitis 5 (mouse)Not determined172461275058612864Mouse
14747010Mancz14_mmandible centroid size 14 (mouse)171199818445998184Mouse
1357680Idd23_minsulin dependent diabetes susceptibility 23 (mouse)Not determined17397489026401133Mouse
4141272Tfv1_mtotal food volume 1 (mouse)Not determined485475265637357Mouse
10412276Leci2_mleukocyte endothelial cell interactions 2 (mouse)Not determined17334817537348299Mouse
1302140Wta4_mweight adult 4 (mouse)Not determined171681972150819843Mouse
1300706Alan1_malloantigen response 1 (mouse)Not determined17485475246469702Mouse
1558886Lgth9_mbody length 9 (mouse)Not determined171506165249061760Mouse
12903990Opfaq5_mopen field activity QTL 5 (mouse)172595092528992098Mouse
4142150Stheal11_msoft tissue heal 11 (mouse)Not determined171228621183361768Mouse
11081168Tir7_mtrypanosome infection response 7 (mouse)171412337248123496Mouse
12910527Nrq1a_mnoise-induced hearing loss resistant QTL 1a (mouse)17129198453Mouse
1301615Cfld3_mcystic fibrosis lung disease 3 (mouse)Not determined17127081639Mouse

Markers in Region
AA998064  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381725,790,638 - 25,790,975UniSTSGRCm38
MGSCv371725,927,583 - 25,927,920UniSTSGRCm37
Celera1726,323,444 - 26,323,781UniSTS
Cytogenetic Map17A3.3UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000095500   ⟹   ENSMUSP00000093155
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1726,005,554 - 26,009,487 (+)Ensembl
GRCm38.p6 Ensembl1725,786,580 - 25,790,513 (+)Ensembl
Ensembl Acc Id: ENSMUST00000235405
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1726,005,554 - 26,009,487 (+)Ensembl
GRCm38.p6 Ensembl1725,786,580 - 25,790,513 (+)Ensembl
RefSeq Acc Id: NM_001165929   ⟹   NP_001159401
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391726,005,554 - 26,009,487 (+)NCBI
GRCm381725,786,580 - 25,790,513 (+)NCBI
MGSCv371725,923,525 - 25,927,458 (+)RGD
Celera1726,319,386 - 26,323,319 (+)RGD
cM Map17 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_017317542   ⟹   XP_017173031
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391726,005,567 - 26,009,208 (+)NCBI
GRCm381725,786,593 - 25,790,257 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001159401 (Get FASTA)   NCBI Sequence Viewer  
  XP_017173031 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein D3Z5T1 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000093155
  ENSMUSP00000093155.5
RefSeq Acc Id: NP_001159401   ⟸   NM_001165929
- UniProtKB: D3Z5T1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017173031   ⟸   XM_017317542
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSMUSP00000093155   ⟸   ENSMUST00000095500

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3Z5T1-F1-model_v2 AlphaFold D3Z5T1 1-437 view protein structure

Promoters
RGD ID:13675178
Promoter ID:EPDNEW_M21738
Type:initiation region
Name:Ccdc78_1
Description:Mus musculus coiled-coil domain containing 78 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381725,786,608 - 25,786,668EPDNEW
RGD ID:6827751
Promoter ID:MM_KWN:22629
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day2,   3T3L1_Day3,   BoneMarrow_0Hour,   Lung
Transcripts:AK140238_CCDC78,   ENSMUST00000095500,   NM_001165929
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361725,922,631 - 25,923,962 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2685784 AgrOrtholog
Ensembl Genes ENSMUSG00000071202 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000095500 ENTREZGENE
  ENSMUST00000095500.5 UniProtKB/Swiss-Prot
InterPro CCDC78 UniProtKB/Swiss-Prot
  DUF4472 UniProtKB/Swiss-Prot
KEGG Report mmu:381077 UniProtKB/Swiss-Prot
MGD MGI:2685784 ENTREZGENE
NCBI Gene 381077 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 78 UniProtKB/Swiss-Prot
  PTHR22106 UniProtKB/Swiss-Prot
Pfam DUF4472 UniProtKB/Swiss-Prot
PhenoGen Ccdc78 PhenoGen
UniProt CCD78_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE