Ccdc65 (coiled-coil domain containing 65) - Rat Genome Database

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Gene: Ccdc65 (coiled-coil domain containing 65) Rattus norvegicus
Analyze
Symbol: Ccdc65
Name: coiled-coil domain containing 65
RGD ID: 1595842
Description: Predicted to be involved in axonemal dynein complex assembly; cilium-dependent cell motility; and regulation of cilium movement. Predicted to be located in ciliary basal body. Predicted to be part of axonemal dynein complex. Predicted to be active in axoneme. Human ortholog(s) of this gene implicated in primary ciliary dyskinesia 27. Orthologous to human CCDC65 (coiled-coil domain containing 65); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: coiled-coil domain-containing protein 65; dynein regulatory complex subunit 2; LOC362994; similar to NYD-SP28 protein
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
GRCr87131,736,002 - 131,749,761 (+)NCBIGRCr8
mRatBN7.27129,857,118 - 129,870,803 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7129,857,247 - 129,870,803 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7131,664,390 - 131,677,788 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07133,889,935 - 133,903,335 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07133,802,444 - 133,815,847 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07140,383,395 - 140,397,186 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7140,383,397 - 140,397,179 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X114,893,569 - 114,907,348 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47137,474,981 - 137,489,918 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7126,346,335 - 126,360,127 (+)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:24094744  


Genomics

Comparative Map Data
Ccdc65
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87131,736,002 - 131,749,761 (+)NCBIGRCr8
mRatBN7.27129,857,118 - 129,870,803 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7129,857,247 - 129,870,803 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7131,664,390 - 131,677,788 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07133,889,935 - 133,903,335 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07133,802,444 - 133,815,847 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.07140,383,395 - 140,397,186 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7140,383,397 - 140,397,179 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X114,893,569 - 114,907,348 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47137,474,981 - 137,489,918 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7126,346,335 - 126,360,127 (+)NCBICelera
Cytogenetic Map7q36NCBI
CCDC65
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381248,904,133 - 48,921,576 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1248,904,110 - 48,931,840 (+)EnsemblGRCh38hg38GRCh38
GRCh371249,297,916 - 49,315,359 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361247,584,197 - 47,601,625 (+)NCBINCBI36Build 36hg18NCBI36
Celera1248,092,267 - 48,109,838 (+)NCBICelera
Cytogenetic Map12q13.12NCBI
HuRef1246,329,756 - 46,347,363 (+)NCBIHuRef
CHM1_11249,263,727 - 49,281,199 (+)NCBICHM1_1
T2T-CHM13v2.01248,866,309 - 48,883,770 (+)NCBIT2T-CHM13v2.0
Ccdc65
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391598,606,075 - 98,621,221 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1598,606,088 - 98,621,217 (+)EnsemblGRCm39 Ensembl
GRCm381598,708,194 - 98,723,340 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1598,708,207 - 98,723,336 (+)EnsemblGRCm38mm10GRCm38
MGSCv371598,538,658 - 98,553,767 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361598,536,261 - 98,551,370 (+)NCBIMGSCv36mm8
Celera15100,856,708 - 100,871,723 (+)NCBICelera
Cytogenetic Map15F1NCBI
cM Map1554.65NCBI
Ccdc65
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555007,733,045 - 7,747,327 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555007,733,054 - 7,744,135 (+)NCBIChiLan1.0ChiLan1.0
CCDC65
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21045,263,470 - 45,279,339 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11245,260,231 - 45,276,283 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01239,829,171 - 39,845,221 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11240,708,937 - 40,723,750 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1240,697,723 - 40,723,750 (-)Ensemblpanpan1.1panPan2
CCDC65
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1275,639,886 - 5,650,140 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl275,639,893 - 5,650,109 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2740,607,677 - 40,617,811 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0275,690,883 - 5,701,009 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl275,689,485 - 5,701,008 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1275,654,819 - 5,664,943 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0275,644,882 - 5,655,006 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02740,999,973 - 41,010,107 (+)NCBIUU_Cfam_GSD_1.0
Ccdc65
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494566,433,256 - 66,443,987 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365126,720,693 - 6,731,478 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365126,720,846 - 6,731,955 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC65
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl514,950,492 - 14,959,327 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1514,949,864 - 14,958,967 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2515,361,365 - 15,368,749 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC65
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11145,146,225 - 45,166,152 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1145,147,199 - 45,165,761 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037200,982,844 - 200,998,419 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc65
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248163,266,395 - 3,280,855 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248163,266,483 - 3,282,580 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc65
128 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:22
Count of miRNA genes:20
Interacting mature miRNAs:21
Transcripts:ENSRNOT00000051186
Prediction methods:Miranda, Pita, 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
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7102297359133492884Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)786983365131983365Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
1357339Stl14Serum triglyceride level QTL 143.450.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7112729683133492707Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7112308254133492884Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat

Markers in Region
AW522737  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,864,791 - 129,864,979 (+)MAPPERmRatBN7.2
Rnor_6.07140,391,385 - 140,391,572NCBIRnor6.0
Rnor_5.0X114,901,547 - 114,901,734UniSTSRnor5.0
RGSC_v3.47137,483,911 - 137,484,098UniSTSRGSC3.4
Celera7126,354,120 - 126,354,307UniSTS
RH 3.4 Map71077.4UniSTS
Cytogenetic Map7q36UniSTS
BE097211  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,861,372 - 129,861,524 (+)MAPPERmRatBN7.2
Rnor_6.07140,387,703 - 140,387,852NCBIRnor6.0
Rnor_5.0X114,897,865 - 114,898,014UniSTSRnor5.0
RGSC_v3.47137,479,821 - 137,479,970UniSTSRGSC3.4
Celera7126,350,579 - 126,350,728UniSTS
RH 3.4 Map71086.5UniSTS
Cytogenetic Map7q36UniSTS
RH136372  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27129,870,460 - 129,870,691 (+)MAPPERmRatBN7.2
Rnor_6.07140,396,844 - 140,397,074NCBIRnor6.0
Rnor_5.0X114,907,006 - 114,907,236UniSTSRnor5.0
RGSC_v3.47137,489,576 - 137,489,806UniSTSRGSC3.4
Celera7126,359,785 - 126,360,015UniSTS
Cytogenetic Map7q36UniSTS


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: ENSRNOT00000090760   ⟹   ENSRNOP00000071850
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7129,857,247 - 129,870,803 (+)Ensembl
Rnor_6.0 Ensembl7140,383,397 - 140,397,179 (+)Ensembl
RefSeq Acc Id: NM_001014203   ⟹   NP_001014225
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87131,736,090 - 131,749,761 (+)NCBI
mRatBN7.27129,857,118 - 129,870,803 (+)NCBI
Rnor_6.07140,383,461 - 140,397,186 (+)NCBI
Rnor_5.0X114,893,569 - 114,907,348 (+)NCBI
RGSC_v3.47137,474,981 - 137,489,918 (+)RGD
Celera7126,346,335 - 126,360,127 (+)RGD
Sequence:
RefSeq Acc Id: XM_063263952   ⟹   XP_063120022
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87131,736,002 - 131,749,036 (+)NCBI
RefSeq Acc Id: XM_063263953   ⟹   XP_063120023
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87131,736,002 - 131,747,789 (+)NCBI
RefSeq Acc Id: XM_063263954   ⟹   XP_063120024
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87131,736,016 - 131,740,524 (+)NCBI
RefSeq Acc Id: NP_001014225   ⟸   NM_001014203
- UniProtKB: Q5XIJ8 (UniProtKB/Swiss-Prot),   A6KC99 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000071850   ⟸   ENSRNOT00000090760
RefSeq Acc Id: XP_063120022   ⟸   XM_063263952
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063120023   ⟸   XM_063263953
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063120024   ⟸   XM_063263954
- Peptide Label: isoform X3
- UniProtKB: A6KCA1 (UniProtKB/TrEMBL)
Protein Domains
Dynein regulatory complex protein 1/2 N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIJ8-F1-model_v2 AlphaFold Q5XIJ8 1-502 view protein structure

Transcriptome

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

Promoters
RGD ID:13695630
Promoter ID:EPDNEW_R6155
Type:multiple initiation site
Name:Ccdc65_1
Description:coiled-coil domain containing 65
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_6.07140,383,403 - 140,383,463EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595842 AgrOrtholog
BioCyc Gene G2FUF-32118 BioCyc
Ensembl Genes ENSRNOG00000058916 Ensembl, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000090760.2 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7135919 IMAGE-MGC_LOAD
InterPro DRC1/2_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  DRC1/DRC2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:362994 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:94536 IMAGE-MGC_LOAD
NCBI Gene 362994 ENTREZGENE
PANTHER DYNEIN REGULATORY COMPLEX SUBUNIT 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NYD-SP28 PROTEIN UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
Pfam NYD-SP28 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ccdc65 PhenoGen
RatGTEx ENSRNOG00000058916 RatGTEx
UniProt A6KC99 ENTREZGENE, UniProtKB/TrEMBL
  A6KCA1 ENTREZGENE, UniProtKB/TrEMBL
  DRC2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Ccdc65  coiled-coil domain containing 65  LOC362994  similar to NYD-SP28 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC362994  similar to NYD-SP28 protein      Symbol and Name status set to provisional 70820 PROVISIONAL