Ccdc180 (coiled-coil domain containing 180) - Rat Genome Database

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Gene: Ccdc180 (coiled-coil domain containing 180) Rattus norvegicus
Analyze
Symbol: Ccdc180
Name: coiled-coil domain containing 180
RGD ID: 6498132
Description: Orthologous to human CCDC180 (coiled-coil domain containing 180); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; dioxygen.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: coiled-coil domain-containing protein 180; LOC100910460; uncharacterized LOC100910460
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2560,154,883 - 60,223,508 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl560,154,910 - 60,223,522 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0561,467,799 - 61,542,675 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl561,474,000 - 61,542,653 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0565,988,737 - 66,057,667 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera558,713,212 - 58,785,674 (+)NCBICelera
Cytogenetic Map5q22NCBI
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
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19056867  


Genomics

Comparative Map Data
Ccdc180
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2560,154,883 - 60,223,508 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl560,154,910 - 60,223,522 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0561,467,799 - 61,542,675 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl561,474,000 - 61,542,653 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0565,988,737 - 66,057,667 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera558,713,212 - 58,785,674 (+)NCBICelera
Cytogenetic Map5q22NCBI
CCDC180
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38997,307,337 - 97,378,751 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl997,307,304 - 97,378,751 (+)EnsemblGRCh38hg38GRCh38
GRCh379100,069,619 - 100,141,033 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera970,584,270 - 70,653,930 (+)NCBICelera
Cytogenetic Map9q22.33NCBI
HuRef969,671,158 - 69,740,837 (+)NCBIHuRef
CHM1_19100,216,353 - 100,286,011 (+)NCBICHM1_1
T2T-CHM13v2.09109,479,282 - 109,550,710 (+)NCBIT2T-CHM13v2.0
Ccdc180
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39445,890,303 - 45,950,774 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl445,890,303 - 45,950,774 (+)EnsemblGRCm39 Ensembl
GRCm38445,890,303 - 45,950,774 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl445,890,303 - 45,950,774 (+)EnsemblGRCm38mm10GRCm38
MGSCv37445,903,175 - 45,963,646 (+)NCBIGRCm37MGSCv37mm9NCBIm37
Celera445,911,888 - 45,972,296 (+)NCBICelera
Cytogenetic Map4B1NCBI
cM Map424.42NCBI
Ccdc180
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541928,002,011 - 28,066,373 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541928,002,063 - 28,066,145 (-)NCBIChiLan1.0ChiLan1.0
CCDC180
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1942,078,381 - 42,169,018 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0968,380,995 - 68,467,787 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1996,502,976 - 96,589,386 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl996,503,785 - 96,589,386 (+)Ensemblpanpan1.1panPan2
CCDC180
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11154,676,397 - 54,740,783 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1154,675,979 - 54,740,428 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1153,104,382 - 53,171,677 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01155,788,214 - 55,856,241 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11154,285,238 - 54,352,547 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01154,315,302 - 54,382,582 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01155,011,900 - 55,079,190 (+)NCBIUU_Cfam_GSD_1.0
Ccdc180
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947169,620,678 - 169,683,391 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365246,168,938 - 6,230,925 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365246,168,334 - 6,230,934 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC180
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1239,209,387 - 239,270,803 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11239,207,628 - 239,275,402 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21267,264,161 - 267,327,361 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC180
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11242,018,614 - 42,154,983 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603839,075,026 - 39,145,861 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc180
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248253,395,735 - 3,447,285 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248253,395,694 - 3,447,623 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc180
199 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:23
Count of miRNA genes:21
Interacting mature miRNAs:23
Transcripts:ENSRNOT00000013930
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
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5228222669540447Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52122674466226744Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)53518915368564008Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)55979352890450144Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat

Markers in Region
AW523240  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2560,172,507 - 60,172,760 (+)MAPPERmRatBN7.2
Rnor_6.0561,491,575 - 61,491,827NCBIRnor6.0
Rnor_5.0566,006,286 - 66,006,538UniSTSRnor5.0
RGSC_v3.4562,421,204 - 62,421,456UniSTSRGSC3.4
Celera558,736,837 - 58,737,089UniSTS
RH 3.4 Map5378.8UniSTS


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 7
Low 2 1 12 1 62 9 11
Below cutoff 3 12 39 29 7 29 5 8 6 15 13 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013930   ⟹   ENSRNOP00000013930
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl560,154,910 - 60,223,522 (+)Ensembl
Rnor_6.0 Ensembl561,474,000 - 61,542,653 (+)Ensembl
RefSeq Acc Id: XM_017593913   ⟹   XP_017449402
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2560,154,967 - 60,223,508 (+)NCBI
Rnor_6.0561,467,799 - 61,542,675 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039111022   ⟹   XP_038966950
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2560,154,883 - 60,223,508 (+)NCBI
Protein Sequences
Protein RefSeqs XP_017449402 (Get FASTA)   NCBI Sequence Viewer  
  XP_038966950 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_017449402   ⟸   XM_017593913
- UniProtKB: F1LXD9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000013930   ⟸   ENSRNOT00000013930
RefSeq Acc Id: XP_038966950   ⟸   XM_039111022
- UniProtKB: F1LXD9 (UniProtKB/TrEMBL)
Protein Domains
DUF4455   DUF4456

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LXD9-F1-model_v2 AlphaFold F1LXD9 1-1647 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:6498132 AgrOrtholog
BioCyc Gene G2FUF-41433 BioCyc
Ensembl Genes ENSRNOG00000010412 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013930 ENTREZGENE
  ENSRNOP00000013930.7 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013930 ENTREZGENE
  ENSRNOT00000013930.7 UniProtKB/TrEMBL
InterPro DUF4455 UniProtKB/TrEMBL
  DUF4456 UniProtKB/TrEMBL
NCBI Gene LOC100910460 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 180 UniProtKB/TrEMBL
  PTHR21444:SF14 UniProtKB/TrEMBL
Pfam DUF4455 UniProtKB/TrEMBL
  DUF4456 UniProtKB/TrEMBL
PhenoGen Ccdc180 PhenoGen
UniProt F1LXD9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-08 Ccdc180  coiled-coil domain containing 180  LOC100910460  uncharacterized LOC100910460  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100910460  uncharacterized LOC100910460      Symbol and Name status set to provisional 70820 PROVISIONAL