Ccdc59 (coiled-coil domain containing 59) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Ccdc59 (coiled-coil domain containing 59) Rattus norvegicus
Analyze
Symbol: Ccdc59
Name: coiled-coil domain containing 59
RGD ID: 1311912
Description: Orthologous to human CCDC59 (coiled-coil domain containing 59); INTERACTS WITH 2,4-dinitrotoluene; bisphenol A; indole-3-methanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC314799; RGD1311912; similar to hypothetical protein D10Ertd718e; thyroid transcription factor 1-associated protein 26
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
GRCr8743,029,272 - 43,035,655 (+)NCBIGRCr8
mRatBN7.2741,142,760 - 41,149,143 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl741,142,760 - 41,149,143 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx743,042,448 - 43,048,836 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0745,245,512 - 45,251,900 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0744,999,901 - 45,006,288 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0747,928,138 - 47,934,690 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl747,928,060 - 47,934,929 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0747,942,423 - 47,948,975 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4744,496,241 - 44,502,624 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1744,516,930 - 44,522,810 (+)NCBI
Celera738,018,929 - 38,025,316 (+)NCBICelera
Cytogenetic Map7q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:22658674  


Genomics

Comparative Map Data
Ccdc59
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8743,029,272 - 43,035,655 (+)NCBIGRCr8
mRatBN7.2741,142,760 - 41,149,143 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl741,142,760 - 41,149,143 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx743,042,448 - 43,048,836 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0745,245,512 - 45,251,900 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0744,999,901 - 45,006,288 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0747,928,138 - 47,934,690 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl747,928,060 - 47,934,929 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0747,942,423 - 47,948,975 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4744,496,241 - 44,502,624 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1744,516,930 - 44,522,810 (+)NCBI
Celera738,018,929 - 38,025,316 (+)NCBICelera
Cytogenetic Map7q21NCBI
CCDC59
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381282,352,303 - 82,358,805 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1282,223,681 - 82,358,805 (-)EnsemblGRCh38hg38GRCh38
GRCh371282,746,082 - 82,752,584 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361281,270,220 - 81,276,330 (-)NCBINCBI36Build 36hg18NCBI36
Celera1282,413,647 - 82,420,144 (-)NCBICelera
Cytogenetic Map12q21.31NCBI
HuRef1279,803,324 - 79,809,821 (-)NCBIHuRef
CHM1_11282,711,940 - 82,718,437 (-)NCBICHM1_1
T2T-CHM13v2.01282,331,767 - 82,338,265 (-)NCBIT2T-CHM13v2.0
Ccdc59
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910105,677,340 - 105,683,371 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10105,676,928 - 105,683,694 (+)EnsemblGRCm39 Ensembl
GRCm3810105,841,479 - 105,847,510 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10105,841,067 - 105,847,833 (+)EnsemblGRCm38mm10GRCm38
MGSCv3710105,278,535 - 105,284,566 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610105,245,589 - 105,251,620 (+)NCBIMGSCv36mm8
Celera10107,790,826 - 107,796,856 (+)NCBICelera
Cytogenetic Map10D1NCBI
cM Map1055.12NCBI
Ccdc59
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540520,731,464 - 20,738,657 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540520,732,649 - 20,738,678 (-)NCBIChiLan1.0ChiLan1.0
CCDC59
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21090,396,588 - 90,402,652 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11290,392,986 - 90,399,103 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01279,864,105 - 79,873,182 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11282,976,079 - 82,981,650 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1282,976,079 - 82,981,650 (-)Ensemblpanpan1.1panPan2
CCDC59
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11524,364,510 - 24,373,567 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1524,364,779 - 24,373,419 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1524,795,481 - 24,804,911 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01524,743,406 - 24,752,836 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1524,743,676 - 24,752,295 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11524,320,972 - 24,330,182 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01524,369,767 - 24,379,043 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01524,610,635 - 24,620,062 (-)NCBIUU_Cfam_GSD_1.0
Ccdc59
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494535,897,608 - 35,905,140 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936507330,481 - 337,906 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936507330,481 - 337,810 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC59
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl599,358,330 - 99,364,091 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1599,358,726 - 99,364,092 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.25104,173,569 - 104,178,937 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC59
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_023666037167,593,487 - 167,599,644 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc59
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248371,686,109 - 1,693,423 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248371,687,403 - 1,693,619 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc59
52 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:362
Count of miRNA genes:215
Interacting mature miRNAs:244
Transcripts:ENSRNOT00000005740
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
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
2303629Vencon3Ventilatory control QTL 37.25respiration trait (VT:0001943)respiration rate (CMO:0000289)74110969256793354Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat


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
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000005740   ⟹   ENSRNOP00000005740
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl741,142,760 - 41,149,143 (+)Ensembl
Rnor_6.0 Ensembl747,928,060 - 47,934,929 (+)Ensembl
RefSeq Acc Id: NM_001108090   ⟹   NP_001101560
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8743,029,272 - 43,035,655 (+)NCBI
mRatBN7.2741,142,760 - 41,149,143 (+)NCBI
Rnor_6.0747,928,138 - 47,934,690 (+)NCBI
Rnor_5.0747,942,423 - 47,948,975 (+)NCBI
RGSC_v3.4744,496,241 - 44,502,624 (+)RGD
Celera738,018,929 - 38,025,316 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101560 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM16780 (Get FASTA)   NCBI Sequence Viewer  
  EDM16781 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000005740.4
RefSeq Acc Id: NP_001101560   ⟸   NM_001108090
- UniProtKB: D4ADF2 (UniProtKB/TrEMBL),   A6IGB7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000005740   ⟸   ENSRNOT00000005740

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ADF2-F1-model_v2 AlphaFold D4ADF2 1-240 view protein structure

Transcriptome

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

Promoters
RGD ID:13695178
Promoter ID:EPDNEW_R5703
Type:multiple initiation site
Name:Ccdc59_1
Description:coiled-coil domain containing 59
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_6.0747,928,546 - 47,928,606EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311912 AgrOrtholog
BioCyc Gene G2FUF-34186 BioCyc
Ensembl Genes ENSRNOG00000004183 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005740.7 UniProtKB/TrEMBL
InterPro rRNA_processing UniProtKB/TrEMBL
KEGG Report rno:314799 UniProtKB/TrEMBL
NCBI Gene 314799 ENTREZGENE
PANTHER PTHR15657 UniProtKB/TrEMBL
  THYROID TRANSCRIPTION FACTOR 1-ASSOCIATED PROTEIN 26 UniProtKB/TrEMBL
Pfam rRNA_processing UniProtKB/TrEMBL
PhenoGen Ccdc59 PhenoGen
PRINTS BR22PROTEIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004183 RatGTEx
UniProt A6IGB7 ENTREZGENE, UniProtKB/TrEMBL
  D4ADF2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ccdc59  coiled-coil domain containing 59   Ccdc59_predicted  coiled-coil domain containing 59 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Ccdc59_predicted  coiled-coil domain containing 59 (predicted)  RGD1311912_predicted  similar to hypothetical protein D10Ertd718e (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1311912_predicted  similar to hypothetical protein D10Ertd718e (predicted)  LOC314799_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC314799_predicted  similar to hypothetical protein D10Ertd718e (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL