Ccdc6 (coiled-coil domain containing 6) - Rat Genome Database

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Gene: Ccdc6 (coiled-coil domain containing 6) Rattus norvegicus
Analyze
Symbol: Ccdc6
Name: coiled-coil domain containing 6
RGD ID: 1587433
Description: Predicted to enable identical protein binding activity. Predicted to be located in cytosol. Orthologous to human CCDC6 (coiled-coil domain containing 6); PARTICIPATES IN thyroid cancer pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 3-chloropropane-1,2-diol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: coiled-coil domain-containing protein 6; LOC691155; similar to coiled-coil domain containing 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82018,431,243 - 18,527,227 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2018,431,243 - 18,527,227 (-)EnsemblGRCr8
mRatBN7.22018,432,177 - 18,528,186 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2018,433,695 - 18,528,658 (-)EnsemblmRatBN7.2
Rnor_6.02019,729,005 - 19,825,219 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2019,732,894 - 19,825,150 (-)Ensemblrn6Rnor6.0
Rnor_5.02021,865,813 - 21,961,494 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42019,160,547 - 19,253,922 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2019,819,225 - 19,915,464 (-)NCBICelera
Cytogenetic Map20p11NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2-methylcholine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-methylcholanthrene  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP,ISO)
amitrole  (EXP)
amphetamine  (EXP)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
bisphenol AF  (ISO)
bortezomib  (ISO)
buspirone  (EXP)
Butylbenzyl phthalate  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
chloropicrin  (ISO)
chlorpyrifos  (ISO)
cisplatin  (ISO)
cobalt dichloride  (ISO)
coumarin  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dimethyl sulfoxide  (ISO)
disodium selenite  (ISO)
doxorubicin  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
etoposide  (ISO)
fenthion  (ISO)
folic acid  (ISO)
FR900359  (ISO)
fulvestrant  (ISO)
gentamycin  (EXP)
hexadecanoic acid  (ISO)
hydrogen peroxide  (ISO)
ivermectin  (ISO)
lead diacetate  (ISO)
leflunomide  (EXP)
levofloxacin  (EXP)
maneb  (ISO)
methyl methanesulfonate  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
Nutlin-3  (ISO)
oxaliplatin  (EXP)
paracetamol  (EXP,ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
rotenone  (EXP,ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
triphenyl phosphate  (ISO)
trovafloxacin  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
zinc protoporphyrin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:37934513  


Genomics

Comparative Map Data
Ccdc6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82018,431,243 - 18,527,227 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2018,431,243 - 18,527,227 (-)EnsemblGRCr8
mRatBN7.22018,432,177 - 18,528,186 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2018,433,695 - 18,528,658 (-)EnsemblmRatBN7.2
Rnor_6.02019,729,005 - 19,825,219 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2019,732,894 - 19,825,150 (-)Ensemblrn6Rnor6.0
Rnor_5.02021,865,813 - 21,961,494 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42019,160,547 - 19,253,922 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2019,819,225 - 19,915,464 (-)NCBICelera
Cytogenetic Map20p11NCBI
CCDC6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381059,788,747 - 59,906,556 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1059,788,747 - 59,907,029 (-)Ensemblhg38GRCh38
GRCh371061,548,505 - 61,666,314 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361061,218,527 - 61,336,824 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341061,218,527 - 61,336,314NCBI
Celera1054,814,284 - 54,932,343 (-)NCBICelera
Cytogenetic Map10q21.2NCBI
HuRef1055,536,106 - 55,653,768 (-)NCBIHuRef
CHM1_11061,830,646 - 61,948,180 (-)NCBICHM1_1
T2T-CHM13v2.01060,642,477 - 60,761,263 (-)NCBIT2T-CHM13v2.0
Ccdc6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391069,932,709 - 70,029,030 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1069,932,951 - 70,029,030 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381070,096,878 - 70,193,200 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1070,097,121 - 70,193,200 (+)Ensemblmm10GRCm38
MGSCv371069,559,869 - 69,655,948 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361069,492,478 - 69,588,557 (+)NCBIMGSCv36mm8
Celera1071,188,144 - 71,284,304 (+)NCBICelera
Cytogenetic Map10B5.3NCBI
cM Map1036.68NCBI
Ccdc6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542513,344,926 - 13,444,802 (-)NCBIChiLan1.0ChiLan1.0
CCDC6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2872,000,268 - 72,118,624 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11072,005,589 - 72,123,475 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01056,322,619 - 56,440,410 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11058,537,553 - 58,655,454 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1058,537,553 - 58,655,454 (-)EnsemblpanPan2panpan1.1
CCDC6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1411,966,366 - 12,077,797 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl411,970,097 - 12,077,484 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha412,163,831 - 12,275,285 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0412,228,962 - 12,340,439 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl412,232,696 - 12,340,130 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1412,209,626 - 12,317,324 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0412,324,478 - 12,435,855 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0412,635,446 - 12,747,202 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ccdc6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721369,006,842 - 69,119,891 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366143,092,882 - 3,394,303 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366143,093,083 - 3,206,147 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1463,175,655 - 63,299,373 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11463,175,650 - 63,300,025 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21468,150,467 - 68,274,633 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1971,382,842 - 71,501,589 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl971,383,032 - 71,497,403 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604832,267,861 - 32,386,892 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247913,718,961 - 3,820,089 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247913,719,006 - 3,822,985 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ccdc6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11816,682,022 - 16,775,710 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ccdc6
739 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:32
Count of miRNA genes:31
Interacting mature miRNAs:32
Transcripts:ENSRNOT00000032159
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804392029865039Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
1598870Bp289Blood pressure QTL 2892.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)20821635953216359Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
1598858Cm61Cardiac mass QTL 613.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)20821635953216359Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)201224324249189476Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000032159   ⟹   ENSRNOP00000033185
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2018,431,243 - 18,527,227 (-)Ensembl
mRatBN7.2 Ensembl2018,433,695 - 18,528,658 (-)Ensembl
Rnor_6.0 Ensembl2019,732,894 - 19,825,150 (-)Ensembl
RefSeq Acc Id: NM_001427373   ⟹   NP_001414302
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82018,431,243 - 18,527,227 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001414302 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000033185
  ENSRNOP00000033185.6
Ensembl Acc Id: ENSRNOP00000033185   ⟸   ENSRNOT00000032159
RefSeq Acc Id: NP_001414302   ⟸   NM_001427373
- UniProtKB: D4AEK9 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AEK9-F1-model_v2 AlphaFold D4AEK9 1-470 view protein structure

Transcriptome

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

Promoters
RGD ID:13701560
Promoter ID:EPDNEW_R12080
Type:initiation region
Name:Ccdc6_1
Description:coiled-coil domain containing 6
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02019,825,220 - 19,825,280EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1587433 AgrOrtholog
BioCyc Gene G2FUF-3979 BioCyc
Ensembl Genes ENSRNOG00000024019 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000032159 ENTREZGENE
  ENSRNOT00000032159.8 UniProtKB/TrEMBL
InterPro DUF2046 UniProtKB/TrEMBL
NCBI Gene 691155 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 6 UniProtKB/TrEMBL
  DUF2046 UniProtKB/TrEMBL
Pfam DUF2046 UniProtKB/TrEMBL
PhenoGen Ccdc6 PhenoGen
RatGTEx ENSRNOG00000024019 RatGTEx
UniProt D4AEK9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Ccdc6  coiled-coil domain containing 6  LOC687820  similar to coiled-coil domain containing 6  Data merged from RGD:1596283 1643240 APPROVED
2008-03-06 Ccdc6  coiled-coil domain containing 6  LOC691155  similar to coiled-coil domain containing 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC687820  similar to coiled-coil domain containing 6      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC691155  similar to coiled-coil domain containing 6      Symbol and Name status set to provisional 70820 PROVISIONAL