Ccdc50 (coiled-coil domain containing 50) - Rat Genome Database

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Gene: Ccdc50 (coiled-coil domain containing 50) Rattus norvegicus
Analyze
Symbol: Ccdc50
Name: coiled-coil domain containing 50
RGD ID: 727841
Description: Predicted to enable ubiquitin protein ligase binding activity. Predicted to act upstream of or within sensory perception of sound. Predicted to be located in cytosol and microtubule cytoskeleton. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 44 and mantle cell lymphoma. Orthologous to human CCDC50 (coiled-coil domain containing 50); INTERACTS WITH 1,2-dimethylhydrazine; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: c3orf6; C3orf6h; coiled-coil domain-containing protein 50; protein Ymer; putative C3orf6 protein; putative C3orf6 protein homolog; putative C3orf6 protein homolog (human)
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
GRCr81186,837,624 - 86,900,164 (-)NCBIGRCr8
mRatBN7.21173,332,798 - 73,395,333 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1173,334,248 - 73,395,150 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1182,171,332 - 82,233,630 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01174,806,362 - 74,868,662 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01173,837,406 - 73,899,757 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01176,742,179 - 76,804,695 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1176,747,865 - 76,804,510 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01183,919,936 - 83,982,339 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41175,302,647 - 75,360,549 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11175,360,235 - 75,418,138 (-)NCBI
Celera1172,269,578 - 72,326,461 (-)NCBICelera
Cytogenetic Map11q22NCBI
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. Gene knockdown studies revealed CCDC50 as a candidate gene in mantle cell lymphoma and chronic lymphocytic leukemia. Farfsing A, etal., Leukemia. 2009 Nov;23(11):2018-26. doi: 10.1038/leu.2009.144. Epub 2009 Jul 30.
2. 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.
3. A mutation in CCDC50, a gene encoding an effector of epidermal growth factor-mediated cell signaling, causes progressive hearing loss. Modamio-Hoybjor S, etal., Am J Hum Genet. 2007 Jun;80(6):1076-89. Epub 2007 Apr 24.
4. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:14527723   PMID:22871113   PMID:23418353  


Genomics

Comparative Map Data
Ccdc50
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81186,837,624 - 86,900,164 (-)NCBIGRCr8
mRatBN7.21173,332,798 - 73,395,333 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1173,334,248 - 73,395,150 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1182,171,332 - 82,233,630 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01174,806,362 - 74,868,662 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01173,837,406 - 73,899,757 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01176,742,179 - 76,804,695 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1176,747,865 - 76,804,510 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01183,919,936 - 83,982,339 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41175,302,647 - 75,360,549 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11175,360,235 - 75,418,138 (-)NCBI
Celera1172,269,578 - 72,326,461 (-)NCBICelera
Cytogenetic Map11q22NCBI
CCDC50
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383191,329,394 - 191,398,659 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3191,329,085 - 191,398,659 (+)EnsemblGRCh38hg38GRCh38
GRCh373191,047,183 - 191,116,448 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363192,529,568 - 192,592,658 (+)NCBINCBI36Build 36hg18NCBI36
Celera3189,475,666 - 189,545,223 (+)NCBICelera
Cytogenetic Map3q28NCBI
HuRef3188,446,586 - 188,516,222 (+)NCBIHuRef
CHM1_13191,010,492 - 191,080,115 (+)NCBICHM1_1
T2T-CHM13v2.03194,145,445 - 194,207,797 (+)NCBIT2T-CHM13v2.0
Ccdc50
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391627,205,815 - 27,270,968 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1627,207,619 - 27,270,968 (+)EnsemblGRCm39 Ensembl
GRCm381627,387,065 - 27,452,218 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1627,388,869 - 27,452,218 (+)EnsemblGRCm38mm10GRCm38
MGSCv371627,389,063 - 27,452,304 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361627,304,216 - 27,364,056 (+)NCBIMGSCv36mm8
Celera1627,928,087 - 27,983,434 (+)NCBICelera
Cytogenetic Map16B2NCBI
cM Map1618.98NCBI
Ccdc50
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542016,891,217 - 16,948,008 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542016,884,985 - 16,948,038 (-)NCBIChiLan1.0ChiLan1.0
CCDC50
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22189,268,461 - 189,331,741 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13189,273,295 - 189,342,953 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03188,621,004 - 188,686,831 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13196,968,825 - 197,038,668 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3196,968,817 - 197,031,790 (+)Ensemblpanpan1.1panPan2
CCDC50
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13423,168,594 - 23,243,221 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3423,168,525 - 23,258,497 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3427,277,632 - 27,334,934 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03423,119,939 - 23,177,337 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.13423,139,896 - 23,197,198 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03423,126,868 - 23,184,645 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03423,369,224 - 23,426,549 (+)NCBIUU_Cfam_GSD_1.0
Ccdc50
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602121,033,853 - 121,101,326 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936900495,547 - 556,316 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936900495,551 - 563,184 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCDC50
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13128,619,230 - 128,690,649 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113128,619,223 - 128,690,964 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213138,015,014 - 138,130,646 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC50
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11585,493,894 - 85,563,412 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1585,494,157 - 85,556,827 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604159,143,858 - 59,213,383 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc50
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473065,882,486 - 65,949,464 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473065,877,175 - 65,949,099 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc50
393 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:29
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000002649
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
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)112952841882566702Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113123913478851519Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113491804179918041Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114094618882566702Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114428575982566702Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114545932375190161Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)115980279482566545Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)115980279482566553Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116611332182169223Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116944607082846715Rat


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 3 40 45 29 19 29 8 10 74 34 38 11 8
Low 3 12 12 12 1 1 3
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000002649   ⟹   ENSRNOP00000002649
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1173,339,992 - 73,378,651 (-)Ensembl
Rnor_6.0 Ensembl1176,747,865 - 76,804,510 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000094418   ⟹   ENSRNOP00000085752
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1173,334,248 - 73,395,150 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000112380   ⟹   ENSRNOP00000087350
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1173,337,512 - 73,395,110 (-)Ensembl
RefSeq Acc Id: NM_001401395   ⟹   NP_001388324
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81186,837,624 - 86,899,980 (-)NCBI
mRatBN7.21173,332,798 - 73,395,154 (-)NCBI
RefSeq Acc Id: NM_182736   ⟹   NP_877400
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81186,837,624 - 86,899,980 (-)NCBI
mRatBN7.21173,332,798 - 73,395,154 (-)NCBI
Rnor_6.01176,747,960 - 76,804,455 (-)NCBI
Rnor_5.01183,919,936 - 83,982,339 (+)NCBI
RGSC_v3.41175,302,647 - 75,360,549 (-)RGD
Celera1172,269,578 - 72,326,461 (-)RGD
Sequence:
RefSeq Acc Id: XM_039088104   ⟹   XP_038944032
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81186,857,603 - 86,900,164 (-)NCBI
mRatBN7.21173,352,776 - 73,395,333 (-)NCBI
RefSeq Acc Id: XR_001840408
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81186,837,628 - 86,900,152 (-)NCBI
mRatBN7.21173,332,798 - 73,395,328 (-)NCBI
Rnor_6.01176,742,179 - 76,804,695 (-)NCBI
Sequence:
RefSeq Acc Id: XR_010055939
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81186,837,628 - 86,900,140 (-)NCBI
RefSeq Acc Id: NP_877400   ⟸   NM_182736
- Peptide Label: isoform 2
- UniProtKB: Q810U0 (UniProtKB/Swiss-Prot),   A0A8I6A494 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000002649   ⟸   ENSRNOT00000002649
RefSeq Acc Id: XP_038944032   ⟸   XM_039088104
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000085752   ⟸   ENSRNOT00000094418
RefSeq Acc Id: ENSRNOP00000087350   ⟸   ENSRNOT00000112380
RefSeq Acc Id: NP_001388324   ⟸   NM_001401395
- Peptide Label: isoform 1
- UniProtKB: A0A8I6GF21 (UniProtKB/TrEMBL)
Protein Domains
Coiled-coil

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q810U0-F1-model_v2 AlphaFold Q810U0 1-305 view protein structure

Transcriptome

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

Promoters
RGD ID:13698234
Promoter ID:EPDNEW_R8759
Type:initiation region
Name:Ccdc50_1
Description:coiled-coil domain containing 50
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_6.01176,804,478 - 76,804,538EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727841 AgrOrtholog
BioCyc Gene G2FUF-20955 BioCyc
Ensembl Genes ENSRNOG00000001930 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00055004555 UniProtKB/Swiss-Prot
  ENSRNOG00060027039 UniProtKB/Swiss-Prot
  ENSRNOG00065003626 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002649.6 UniProtKB/TrEMBL
  ENSRNOT00000094418 ENTREZGENE
  ENSRNOT00000094418.1 UniProtKB/TrEMBL
  ENSRNOT00000112380 ENTREZGENE
  ENSRNOT00000112380.1 UniProtKB/TrEMBL
  ENSRNOT00055007218 UniProtKB/Swiss-Prot
  ENSRNOT00060047256 UniProtKB/Swiss-Prot
  ENSRNOT00065005279 UniProtKB/Swiss-Prot
InterPro CCDC50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CCDC50_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:288022 UniProtKB/Swiss-Prot
NCBI Gene 288022 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 50 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR22115 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CCDC50_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ccdc50 PhenoGen
RatGTEx ENSRNOG00000001930 RatGTEx
  ENSRNOG00055004555 RatGTEx
  ENSRNOG00060027039 RatGTEx
  ENSRNOG00065003626 RatGTEx
UniProt A0A8I6A494 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GF21 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2Q0J1_RAT UniProtKB/TrEMBL
  CCD50_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-03 Ccdc50  coiled-coil domain containing 50  C3orf6h  putative C3orf6 protein homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 c3orf6h  putative C3orf6 protein homolog (human)  c3orf6  putative C3orf6 protein  Symbol and Name updated 1299863 APPROVED