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

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Gene: Ccdc78 (coiled-coil domain containing 78) Rattus norvegicus
Analyze
Symbol: Ccdc78
Name: coiled-coil domain containing 78
RGD ID: 1560244
Description: Predicted to be involved in de novo centriole assembly involved in multi-ciliated epithelial cell differentiation and skeletal muscle contraction. Predicted to be located in several cellular components, including centriole; deuterosome; and sarcolemma. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in centronuclear myopathy 4. Orthologous to human CCDC78 (coiled-coil domain containing 78); INTERACTS WITH 1,2-dimethylhydrazine; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: coiled-coil domain-containing protein 78; LOC302996; RGD1560244; similar to hypothetical protein FLJ34512
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:20577004   PMID:22818856   PMID:24075808  


Genomics

Comparative Map Data
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
(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
(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
(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
16 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:168
Count of miRNA genes:112
Interacting mature miRNAs:129
Transcripts:ENSRNOT00000020363
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat

Markers in Region
AA998064  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21014,812,411 - 14,812,749 (+)MAPPERmRatBN7.2
Rnor_6.01015,160,167 - 15,160,504NCBIRnor6.0
Rnor_5.01014,973,110 - 14,973,447UniSTSRnor5.0
RGSC_v3.41015,057,810 - 15,058,147UniSTSRGSC3.4
Celera1014,481,388 - 14,481,725UniSTS
RH 3.4 Map10151.66UniSTS
Cytogenetic Map10q12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
6 11 47 108 46 50 20 21 20 6 163 86 93 43 58 30

Sequence


Ensembl Acc Id: ENSRNOT00000020363   ⟹   ENSRNOP00000020363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1014,807,710 - 14,812,282 (+)Ensembl
Rnor_6.0 Ensembl1015,156,207 - 15,159,894 (+)Ensembl
RefSeq Acc Id: XM_039087110   ⟹   XP_038943038
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,312,403 - 15,316,800 (+)NCBI
mRatBN7.21014,808,356 - 14,812,284 (+)NCBI
RefSeq Acc Id: XM_063270093   ⟹   XP_063126163
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,312,422 - 15,316,800 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001417115 (Get FASTA)   NCBI Sequence Viewer  
  NP_001417116 (Get FASTA)   NCBI Sequence Viewer  
  XP_038943038 (Get FASTA)   NCBI Sequence Viewer  
  XP_063126163 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68182 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000020363.7
Ensembl Acc Id: ENSRNOP00000020363   ⟸   ENSRNOT00000020363
RefSeq Acc Id: XP_038943038   ⟸   XM_039087110
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063126163   ⟸   XM_063270093
- Peptide Label: isoform X1
Protein Domains
DUF4472

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F7ELZ7-F1-model_v2 AlphaFold F7ELZ7 1-425 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560244 AgrOrtholog
BioCyc Gene G2FUF-25760 BioCyc
Ensembl Genes ENSRNOG00000022331 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020363.7 UniProtKB/TrEMBL
InterPro CCDC78 UniProtKB/TrEMBL
  DUF4472 UniProtKB/TrEMBL
NCBI Gene 302996 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 78 UniProtKB/TrEMBL
  PTHR22106 UniProtKB/TrEMBL
Pfam DUF4472 UniProtKB/TrEMBL
PhenoGen Ccdc78 PhenoGen
RatGTEx ENSRNOG00000022331 RatGTEx
Superfamily-SCOP Formin homology 2 domain (FH2 domain) UniProtKB/TrEMBL
UniProt F7ELZ7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-11 Ccdc78  coiled-coil domain containing 78  RGD1560244  similar to hypothetical protein FLJ34512  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1560244  similar to hypothetical protein FLJ34512   RGD1560244_predicted  similar to hypothetical protein FLJ34512 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560244_predicted  similar to hypothetical protein FLJ34512 (predicted)  LOC302996  similar to hypothetical protein FLJ34512  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302996  similar to hypothetical protein FLJ34512      Symbol and Name status set to provisional 70820 PROVISIONAL