Cenpc (centromere protein C) - 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   new 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
Gene: Cenpc (centromere protein C) Rattus norvegicus
Analyze
Symbol: Cenpc
Name: centromere protein C
RGD ID: 1303061
Description: Predicted to enable centromeric DNA binding activity and identical protein binding activity. Predicted to be involved in attachment of mitotic spindle microtubules to kinetochore; kinetochore assembly; and spindle attachment to meiosis I kinetochore. Predicted to be located in kinetochore; midbody; and nuclear body. Predicted to be part of inner kinetochore and pericentric heterochromatin. Human ortholog(s) of this gene implicated in CREST syndrome and liver cirrhosis. Orthologous to human CENPC (centromere protein C); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Cenpc1; centromere autoantigen C; centromere protein C 1; centromere protein C1
RGD Orthologs
Human
Mouse
Chinchilla
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
GRCr81422,342,910 - 22,401,522 (+)NCBIGRCr8
mRatBN7.21421,988,067 - 22,046,732 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1421,988,144 - 22,055,476 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1422,344,912 - 22,404,654 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01423,657,349 - 23,717,084 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01422,188,431 - 22,248,172 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01423,611,909 - 23,670,314 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1423,611,735 - 23,670,475 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01423,515,129 - 23,571,976 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41423,771,576 - 23,829,980 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11423,771,575 - 23,829,977 (+)NCBI
Celera1421,462,361 - 21,520,618 (+)NCBICelera
Cytogenetic Map14p21NCBI
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. Diversity of humoral responses to the centromere proteins among HCV-related chronic liver disease, PBC and AIH patients. Himoto T, etal., Clin Res Hepatol Gastroenterol. 2015 Apr;39(2):222-9. doi: 10.1016/j.clinre.2014.08.004. Epub 2014 Sep 15.
3. Gene structure and sequence analysis of mouse centromere proteins A and C. Kalitsis P, etal., Genomics 1998 Jan 1;47(1):108-14.
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:11682612   PMID:15242786   PMID:15345035   PMID:19503796   PMID:21529714  


Genomics

Comparative Map Data
Cenpc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81422,342,910 - 22,401,522 (+)NCBIGRCr8
mRatBN7.21421,988,067 - 22,046,732 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1421,988,144 - 22,055,476 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1422,344,912 - 22,404,654 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01423,657,349 - 23,717,084 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01422,188,431 - 22,248,172 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01423,611,909 - 23,670,314 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1423,611,735 - 23,670,475 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01423,515,129 - 23,571,976 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41423,771,576 - 23,829,980 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11423,771,575 - 23,829,977 (+)NCBI
Celera1421,462,361 - 21,520,618 (+)NCBICelera
Cytogenetic Map14p21NCBI
CENPC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38467,468,762 - 67,545,503 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl467,468,762 - 67,545,503 (-)EnsemblGRCh38hg38GRCh38
GRCh37468,334,480 - 68,411,221 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36468,020,584 - 68,093,851 (-)NCBINCBI36Build 36hg18NCBI36
Build 34468,166,961 - 68,239,995NCBI
Celera465,800,619 - 65,873,659 (-)NCBICelera
Cytogenetic Map4q13.2NCBI
HuRef464,251,196 - 64,324,430 (-)NCBIHuRef
CHM1_1468,375,177 - 68,448,439 (-)NCBICHM1_1
T2T-CHM13v2.0470,911,881 - 70,988,601 (-)NCBIT2T-CHM13v2.0
Cenpc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39586,159,877 - 86,214,325 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl586,159,883 - 86,213,442 (-)EnsemblGRCm39 Ensembl
GRCm38586,012,018 - 86,065,962 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl586,012,024 - 86,065,583 (-)EnsemblGRCm38mm10GRCm38
MGSCv37586,441,049 - 86,494,608 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36587,086,585 - 87,140,032 (-)NCBIMGSCv36mm8
Celera583,243,963 - 83,297,482 (-)NCBICelera
Cytogenetic Map5E1NCBI
cM Map543.56NCBI
Cenpc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554475,345,896 - 5,406,730 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554475,345,617 - 5,406,889 (+)NCBIChiLan1.0ChiLan1.0
CENPC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11358,013,218 - 58,091,347 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1358,013,212 - 58,231,200 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1357,928,845 - 58,006,993 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01358,634,688 - 58,702,538 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1358,634,844 - 58,702,350 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11358,350,980 - 58,428,821 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01357,841,062 - 57,919,053 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01358,850,883 - 58,929,219 (-)NCBIUU_Cfam_GSD_1.0
Cenpc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528518,357,663 - 18,414,077 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936582920,833 - 981,373 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936582920,852 - 978,167 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CENPC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl865,238,090 - 65,315,713 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1865,237,825 - 65,315,788 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2869,658,715 - 69,740,181 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CENPC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.171,393,336 - 1,464,189 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl71,393,348 - 1,467,989 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660661,480,301 - 1,552,594 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cenpc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247611,422,857 - 1,498,726 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cenpc
306 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:180
Count of miRNA genes:132
Interacting mature miRNAs:141
Transcripts:ENSRNOT00000031074
Prediction methods:Microtar, Miranda, 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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat


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 2 29 37 22 19 22 2 2 74 25 39 11 2
Low 1 14 20 19 19 6 8 10 2 6
Below cutoff 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000031074   ⟹   ENSRNOP00000032986
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1421,988,144 - 22,046,729 (+)Ensembl
Rnor_6.0 Ensembl1423,611,735 - 23,670,475 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101440   ⟹   ENSRNOP00000090600
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1421,988,144 - 22,046,729 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113695   ⟹   ENSRNOP00000093827
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1421,988,144 - 22,055,476 (+)Ensembl
RefSeq Acc Id: NM_001004098   ⟹   NP_001004098
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81422,343,115 - 22,401,522 (+)NCBI
mRatBN7.21421,988,320 - 22,046,732 (+)NCBI
Rnor_6.01423,611,909 - 23,670,314 (+)NCBI
Rnor_5.01423,515,129 - 23,571,976 (+)NCBI
RGSC_v3.41423,771,576 - 23,829,980 (+)RGD
Celera1421,462,361 - 21,520,618 (+)RGD
Sequence:
RefSeq Acc Id: XM_039091875   ⟹   XP_038947803
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81422,342,910 - 22,401,522 (+)NCBI
mRatBN7.21421,988,067 - 22,046,726 (+)NCBI
RefSeq Acc Id: XM_063273074   ⟹   XP_063129144
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81422,356,276 - 22,401,522 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001004098   ⟸   NM_001004098
- UniProtKB: Q66LH7 (UniProtKB/TrEMBL),   E9PSW8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000032986   ⟸   ENSRNOT00000031074
RefSeq Acc Id: XP_038947803   ⟸   XM_039091875
- Peptide Label: isoform X1
- UniProtKB: E9PSW8 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000093827   ⟸   ENSRNOT00000113695
RefSeq Acc Id: ENSRNOP00000090600   ⟸   ENSRNOT00000101440
RefSeq Acc Id: XP_063129144   ⟸   XM_063273074
- Peptide Label: isoform X2
Protein Domains
CENP-C middle DNMT3B-binding   Kinetochore assembly subunit CENP-C N-terminal   Mif2/CENP-C cupin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-E9PSW8-F1-model_v2 AlphaFold E9PSW8 1-916 view protein structure

Transcriptome

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

Promoters
RGD ID:13699261
Promoter ID:EPDNEW_R9786
Type:initiation region
Name:Cenpc_1
Description:centromere protein C
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_6.01423,611,766 - 23,611,826EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303061 AgrOrtholog
BioCyc Gene G2FUF-16062 BioCyc
Ensembl Genes ENSRNOG00000021776 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031074 ENTREZGENE
  ENSRNOT00000031074.6 UniProtKB/TrEMBL
  ENSRNOT00000101440.1 UniProtKB/TrEMBL
  ENSRNOT00000113695.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.10 UniProtKB/TrEMBL
InterPro CENP-C/Mif2/cnp3 UniProtKB/TrEMBL
  CENP-C_mid UniProtKB/TrEMBL
  CENP_C_N_dom UniProtKB/TrEMBL
  Cupin_RmlC_type UniProtKB/TrEMBL
  Mif2/CENP-C_cupin UniProtKB/TrEMBL
  RmlC-like_jellyroll UniProtKB/TrEMBL
KEGG Report rno:305270 UniProtKB/TrEMBL
NCBI Gene 305270 ENTREZGENE
PANTHER CENTROMERE PROTEIN C UniProtKB/TrEMBL
  PTHR16684 UniProtKB/TrEMBL
Pfam CENP-C_mid UniProtKB/TrEMBL
  CENP_C_N UniProtKB/TrEMBL
  Mif2 UniProtKB/TrEMBL
PhenoGen Cenpc PhenoGen
RatGTEx ENSRNOG00000021776 RatGTEx
Superfamily-SCOP RmlC_like_cupin UniProtKB/TrEMBL
UniProt A0A8I6ACV2_RAT UniProtKB/TrEMBL
  E9PSW8 ENTREZGENE, UniProtKB/TrEMBL
  Q66LH7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-07-18 Cenpc  centromere protein C  Cenpc1  centromere protein C1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-07-10 Cenpc1  centromere protein C1  Cenpc1  centromere protein C 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Cenpc1  centromere protein C 1      Symbol and Name status set to approved 1299863 APPROVED
2005-01-07 Cenpc1  centromere protein C 1  Cenpc  centromere autoantigen C  Symbol and Name updated 1299863 PENDING