Ccdc3 (coiled-coil domain containing 3) - Rat Genome Database

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Gene: Ccdc3 (coiled-coil domain containing 3) Rattus norvegicus
Analyze
Symbol: Ccdc3
Name: coiled-coil domain containing 3
RGD ID: 1559473
Description: Predicted to be involved in several processes, including negative regulation of gene expression; negative regulation of lipid metabolic process; and negative regulation of tumor necrosis factor-mediated signaling pathway. Predicted to act upstream of or within negative regulation of lipid biosynthetic process; positive regulation of fat cell differentiation; and positive regulation of lipid biosynthetic process. Predicted to be located in endoplasmic reticulum. Predicted to be active in extracellular region. Orthologous to human CCDC3 (coiled-coil domain containing 3); INTERACTS WITH (+)-schisandrin B; bisphenol A; dibutyl phthalate.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: coiled-coil domain-containing protein 3; LOC498795; RGD1559473; similar to Coiled-coil domain containing protein 3 precursor
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
GRCr81777,941,148 - 78,044,820 (-)NCBIGRCr8
mRatBN7.21773,031,891 - 73,135,173 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1773,035,045 - 73,135,337 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01776,991,722 - 77,093,515 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1776,995,043 - 77,093,308 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01778,644,571 - 78,747,680 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41784,115,413 - 84,219,015 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1772,479,624 - 72,576,235 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. 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:25193116   PMID:25605713   PMID:28827783  


Genomics

Comparative Map Data
Ccdc3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81777,941,148 - 78,044,820 (-)NCBIGRCr8
mRatBN7.21773,031,891 - 73,135,173 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1773,035,045 - 73,135,337 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01776,991,722 - 77,093,515 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1776,995,043 - 77,093,308 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01778,644,571 - 78,747,680 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41784,115,413 - 84,219,015 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1772,479,624 - 72,576,235 (-)NCBICelera
Cytogenetic Map17q12.3NCBI
CCDC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381012,896,625 - 13,099,989 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1012,896,625 - 13,099,652 (-)EnsemblGRCh38hg38GRCh38
GRCh371012,938,625 - 13,141,989 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361012,978,631 - 13,083,710 (-)NCBINCBI36Build 36hg18NCBI36
Build 341012,978,632 - 13,083,710NCBI
Celera1012,864,409 - 12,969,462 (-)NCBICelera
Cytogenetic Map10p13NCBI
HuRef1012,851,677 - 12,956,755 (-)NCBIHuRef
CHM1_11012,938,663 - 13,043,722 (-)NCBICHM1_1
T2T-CHM13v2.01012,911,015 - 13,114,320 (-)NCBIT2T-CHM13v2.0
Ccdc3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3925,142,587 - 5,235,682 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl25,142,587 - 5,235,689 (+)EnsemblGRCm39 Ensembl
GRCm3825,137,311 - 5,235,967 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl25,137,776 - 5,230,878 (+)EnsemblGRCm38mm10GRCm38
MGSCv3725,058,822 - 5,151,917 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3625,055,048 - 5,148,143 (+)NCBIMGSCv36mm8
Celera25,092,620 - 5,185,508 (+)NCBICelera
Cytogenetic Map2A1NCBI
cM Map23.25NCBI
Ccdc3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955462909,300 - 1,013,927 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955462909,300 - 1,013,927 (-)NCBIChiLan1.0ChiLan1.0
CCDC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2825,364,879 - 25,624,888 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11025,370,261 - 25,630,217 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01012,901,592 - 13,104,528 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11012,875,678 - 13,077,658 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1012,875,678 - 13,025,280 (-)Ensemblpanpan1.1panPan2
CCDC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1223,477,696 - 23,593,107 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl223,477,696 - 23,591,036 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha220,496,338 - 20,611,642 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0223,849,850 - 23,965,174 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl223,849,972 - 23,965,171 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1220,976,448 - 21,091,609 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0221,818,806 - 21,933,920 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0222,535,216 - 22,650,552 (+)NCBIUU_Cfam_GSD_1.0
Ccdc3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934426,290,662 - 26,402,310 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364842,455,819 - 2,568,682 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364842,455,819 - 2,567,467 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100510975
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1059,052,915 - 59,144,797 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11059,052,979 - 59,144,791 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21064,772,802 - 64,846,901 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1912,940,629 - 13,091,520 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605118,462,890 - 18,566,080 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248055,465,001 - 5,574,291 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248055,465,699 - 5,574,837 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc3
1259 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:98
Count of miRNA genes:84
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000024110
Prediction methods:Microtar, 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
1358295Aocep1Aortic cell protein QTL 16.17e-07thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176570358081153923Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175349882882479847Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176261951686533673Rat
9590107Sffal7Serum free fatty acids level QTL 74.810.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)172840914773409147Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)174992015486533673Rat
724549Niddm56Non-insulin dependent diabetes mellitus QTL 560.03blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)173199078476990784Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
2317045Aia11Adjuvant induced arthritis QTL 114.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)176078142686533673Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
8552928Pigfal9Plasma insulin-like growth factor 1 level QTL 99blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)172840914773409147Rat
12904736Cm121Cardiac mass QTL 1210.043heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)177177462182479847Rat
1300148Bp192Blood pressure QTL 1923.47arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)173455084373951021Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175090909986022412Rat
2324621Coatc5Coat color QTL 5coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)173136839173951021Rat
1300131Bp193Blood pressure QTL 1933.3arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)176364000973951021Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)175900564977910000Rat
1300129Rf25Renal function QTL 253.03blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)177100332581153923Rat
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)175724684382046127Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175004027186533673Rat

Markers in Region
RH132647  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21773,035,070 - 73,035,286 (+)MAPPERmRatBN7.2
Rnor_6.01776,993,444 - 76,993,659NCBIRnor6.0
Rnor_5.01778,646,293 - 78,646,508UniSTSRnor5.0
RGSC_v3.41784,115,463 - 84,115,678UniSTSRGSC3.4
Celera1772,481,346 - 72,481,561UniSTS
RH 3.4 Map17724.9UniSTS
Cytogenetic Map17q12.3UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 12 4 2 21 23 6
Low 3 31 47 35 11 35 8 11 68 14 18 5 8
Below cutoff 6 6 6 6 6

Sequence


RefSeq Acc Id: ENSRNOT00000024110   ⟹   ENSRNOP00000024110
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1773,035,045 - 73,135,337 (-)Ensembl
Rnor_6.0 Ensembl1776,995,043 - 77,093,308 (-)Ensembl
RefSeq Acc Id: XM_574081   ⟹   XP_574081
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81777,941,148 - 78,044,820 (-)NCBI
mRatBN7.21773,031,891 - 73,135,173 (-)NCBI
Rnor_6.01776,991,722 - 77,093,515 (-)NCBI
Rnor_5.01778,644,571 - 78,747,680 (-)NCBI
RGSC_v3.41784,115,413 - 84,219,015 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_574081 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL78665 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000024110.3
RefSeq Acc Id: XP_574081   ⟸   XM_574081
- UniProtKB: D3ZAR0 (UniProtKB/TrEMBL),   A6JLY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024110   ⟸   ENSRNOT00000024110

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZAR0-F1-model_v2 AlphaFold D3ZAR0 1-273 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:1559473 AgrOrtholog
BioCyc Gene G2FUF-8694 BioCyc
Ensembl Genes ENSRNOG00000017933 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000024110.5 UniProtKB/TrEMBL
InterPro CCDC3 UniProtKB/TrEMBL
KEGG Report rno:498795 UniProtKB/TrEMBL
NCBI Gene 498795 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 3 UniProtKB/TrEMBL
  PTHR31663 UniProtKB/TrEMBL
PhenoGen Ccdc3 PhenoGen
RatGTEx ENSRNOG00000017933 RatGTEx
UniProt A6JLY8 ENTREZGENE, UniProtKB/TrEMBL
  D3ZAR0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Ccdc3  coiled-coil domain containing 3  RGD1559473_predicted  similar to Coiled-coil domain containing protein 3 precursor (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1559473_predicted  similar to Coiled-coil domain containing protein 3 precursor (predicted)  LOC498795  similar to Coiled-coil domain containing protein 3 precursor  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498795  similar to Coiled-coil domain containing protein 3 precursor      Symbol and Name status set to provisional 70820 PROVISIONAL