Ccdc127 (coiled-coil domain containing 127) - 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 Behavioral & Substance Use Disorder 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: Ccdc127 (coiled-coil domain containing 127) Rattus norvegicus
Analyze
Symbol: Ccdc127
Name: coiled-coil domain containing 127
RGD ID: 735106
Description: Predicted to be involved in lipid homeostasis. Predicted to be located in mitochondrial outer membrane. Orthologous to human CCDC127 (coiled-coil domain containing 127); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 3,4-methylenedioxymethamphetamine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: coiled-coil domain-containing protein 127; MGC73017; RGD735106; similar to RIKEN cDNA 0610011N22 gene; Unknown (protein for MGC:73017)
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
GRCr8130,757,010 - 30,764,473 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl130,757,010 - 30,764,473 (-)EnsemblGRCr8
mRatBN7.2128,928,420 - 28,935,885 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl128,928,325 - 28,935,893 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx128,729,576 - 28,737,057 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0134,729,430 - 34,736,919 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0128,930,198 - 28,937,687 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0131,538,088 - 31,545,573 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl131,539,215 - 31,545,559 (-)Ensemblrn6Rnor6.0
Rnor_5.0132,964,236 - 32,971,719 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4129,732,942 - 29,739,285 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera127,581,393 - 27,587,727 (-)NCBICelera
RGSC_v3.1129,735,887 - 29,742,230 (-)NCBI
Cytogenetic Map1p11NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
lipid homeostasis  (ISO,ISS)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334   PMID:34800366  


Genomics

Comparative Map Data
Ccdc127
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8130,757,010 - 30,764,473 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl130,757,010 - 30,764,473 (-)EnsemblGRCr8
mRatBN7.2128,928,420 - 28,935,885 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl128,928,325 - 28,935,893 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx128,729,576 - 28,737,057 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0134,729,430 - 34,736,919 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0128,930,198 - 28,937,687 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0131,538,088 - 31,545,573 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl131,539,215 - 31,545,559 (-)Ensemblrn6Rnor6.0
Rnor_5.0132,964,236 - 32,971,719 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4129,732,942 - 29,739,285 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera127,581,393 - 27,587,727 (-)NCBICelera
RGSC_v3.1129,735,887 - 29,742,230 (-)NCBI
Cytogenetic Map1p11NCBI
CCDC127
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385196,868 - 218,153 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5196,868 - 218,153 (-)Ensemblhg38GRCh38
GRCh375196,983 - 218,268 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 365257,875 - 271,297 (-)NCBIBuild 36Build 36hg18NCBI36
Celera5304,440 - 317,859 (-)NCBICelera
Cytogenetic Map5p15.33NCBI
HuRef5194,636 - 208,187 (-)NCBIHuRef
CHM1_15203,485 - 215,672 (-)NCBICHM1_1
T2T-CHM13v2.05188,246 - 209,196 (-)NCBIT2T-CHM13v2.0
Ccdc127
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391374,498,436 - 74,513,902 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1374,498,428 - 74,513,902 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381374,350,317 - 74,365,783 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1374,350,309 - 74,365,783 (+)Ensemblmm10GRCm38
MGSCv371374,487,765 - 74,503,231 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361374,816,367 - 74,825,663 (+)NCBIMGSCv36mm8
Celera1376,679,653 - 76,696,001 (+)NCBICelera
Cytogenetic Map13C1NCBI
cM Map1340.17NCBI
Ccdc127
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495550416,843 - 36,810 (-)Ensembl
ChiLan1.0NW_00495550417,499 - 36,804 (-)NCBIChiLan1.0ChiLan1.0
CCDC127
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v24423,385 - 434,038 (-)NCBINHGRI_mPanPan1-v2
PanPan1.1 Ensembl5343,849 - 354,260 (-)EnsemblpanPan2panpan1.1
CCDC127
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13411,965,098 - 11,976,233 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3411,964,439 - 11,976,037 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3416,478,268 - 16,489,477 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03411,866,740 - 11,877,895 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3411,866,695 - 11,877,892 (+)EnsemblROS_Cfam_1.0 Ensembl
UNSW_CanFamBas_1.03411,905,721 - 11,916,878 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03412,107,746 - 12,118,966 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ccdc127
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213245,012,444 - 245,021,133 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049368151,175,275 - 1,186,524 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049368151,174,345 - 1,182,418 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC127
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1679,862,686 - 79,870,755 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11679,862,594 - 79,870,525 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CCDC127
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.14151,804 - 163,644 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl4147,662 - 163,588 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366697213,997 - 24,227 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc127
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475136,890 - 54,710 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475137,849 - 54,810 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Ccdc127
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12203,777,827 - 203,784,340 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ccdc127
23 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:262
Count of miRNA genes:172
Interacting mature miRNAs:196
Transcripts:ENSRNOT00000017779
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)1529322934184556Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1774611852746118Rat
4889451Eae29Experimental allergic encephalomyelitis QTL 295.51nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1774612152746121Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12940927974409279Rat
70179Xhs2X-ray hypersensitivity QTL 23.2intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)1143965634Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)11037949255379492Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1694102251941022Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1529322934184556Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)1690935351909353Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11731537851816258Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)1690935351909353Rat
5684999Bss102Bone structure and strength QTL 1025.57e-07tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)1690935351909353Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11282049457820494Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)1134184556Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)12065642065656420Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)12050832665508326Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)11168446456684464Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)13070837587558729Rat
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1529322934184556Rat


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 89 59 6 353 189 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000017779   ⟹   ENSRNOP00000017779
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl131,539,215 - 31,545,559 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098265   ⟹   ENSRNOP00000088745
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl130,757,010 - 30,764,473 (-)Ensembl
mRatBN7.2 Ensembl128,928,325 - 28,935,893 (-)Ensembl
RefSeq Acc Id: NM_198766   ⟹   NP_942061
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8130,757,010 - 30,764,473 (-)NCBI
mRatBN7.2128,928,420 - 28,935,885 (-)NCBI
Rnor_6.0131,539,214 - 31,545,557 (-)NCBI
Rnor_5.0132,964,236 - 32,971,719 (-)NCBI
RGSC_v3.4129,732,942 - 29,739,285 (-)RGD
Celera127,581,393 - 27,587,727 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_942061 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH58157 (Get FASTA)   NCBI Sequence Viewer  
  EDL87685 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000088745
GenBank Protein Q6PEB9 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_942061   ⟸   NM_198766
- UniProtKB: Q6PEB9 (UniProtKB/Swiss-Prot),   A0A8I6A8F9 (UniProtKB/TrEMBL),   A6JUU4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000017779   ⟸   ENSRNOT00000017779
Ensembl Acc Id: ENSRNOP00000088745   ⟸   ENSRNOT00000098265

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6PEB9-F1-model_v2 AlphaFold Q6PEB9 1-260 view protein structure

Transcriptome

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

Promoters
RGD ID:13689553
Promoter ID:EPDNEW_R78
Type:multiple initiation site
Name:Ccdc127_1
Description:coiled-coil domain containing 127
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_6.0131,545,536 - 31,545,596EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735106 AgrOrtholog
BioCyc Gene G2FUF-61947 BioCyc
Ensembl Genes ENSRNOG00000012775 Ensembl
  ENSRNOG00000066093 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000098265 ENTREZGENE
IMAGE_CLONE IMAGE:6890640 IMAGE-MGC_LOAD
InterPro CCDC127 UniProtKB/Swiss-Prot
KEGG Report rno:308060 UniProtKB/Swiss-Prot
MGC_CLONE MGC:73017 IMAGE-MGC_LOAD
NCBI Gene 308060 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 127 UniProtKB/Swiss-Prot
  PTHR31958 UniProtKB/Swiss-Prot
PhenoGen Ccdc127 PhenoGen
RatGTEx ENSRNOG00000012775 RatGTEx
  ENSRNOG00000066093 RatGTEx
UniProt A0A8I6A8F9 ENTREZGENE, UniProtKB/TrEMBL
  A6JUU4 ENTREZGENE, UniProtKB/TrEMBL
  CC127_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Ccdc127  coiled-coil domain containing 127  RGD735106  similar to RIKEN cDNA 0610011N22 gene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-11-17 RGD735106  similar to RIKEN cDNA 0610011N22 gene  MGC73017  Unknown (protein for MGC:73017)  Symbol and Name updated 1299863 APPROVED
2005-10-12 MGC73017        Symbol and Name status set to provisional 70820 PROVISIONAL