Cenpb (centromere protein B) - 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: Cenpb (centromere protein B) Rattus norvegicus
Analyze
Symbol: Cenpb
Name: centromere protein B
RGD ID: 1304794
Description: Predicted to enable DNA binding activity. Predicted to be located in condensed chromosome, centromeric region; nuclear body; and pericentric heterochromatin. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in inner ear disease and primary biliary cholangitis. Orthologous to human CENPB (centromere protein B); INTERACTS WITH 2,4-dinitrotoluene; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: centromere autoantigen B; LOC362217; major centromere autoantigen B
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
GRCr83138,850,003 - 138,852,796 (-)NCBIGRCr8
mRatBN7.23118,396,987 - 118,399,780 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3118,388,546 - 118,400,470 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3122,291,319 - 122,294,112 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03130,890,684 - 130,893,477 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03128,547,420 - 128,550,213 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03123,720,888 - 123,723,520 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3123,721,486 - 123,723,524 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03130,219,280 - 130,221,879 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43118,883,667 - 118,886,327 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13118,789,239 - 118,791,848 (-)NCBI
Celera3117,205,145 - 117,207,804 (-)NCBICelera
Cytogenetic Map3q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Audiovestibular manifestations in patients with limited systemic sclerosis and centromere protein-B (CENP-B) antibodies. Amor-Dorado JC, etal., Medicine (Baltimore). 2008 May;87(3):131-41. doi: 10.1097/MD.0b013e318173aa56.
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. [Clinical significance of anti-centromere antibody and anti-CENP-B antibody in sera of patients with primary biliary cirrhosis]. Onozuka Y, etal., Rinsho Byori. 1996 Sep;44(9):877-82.
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:2022189   PMID:11084331   PMID:11682612   PMID:15242786  


Genomics

Comparative Map Data
Cenpb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83138,850,003 - 138,852,796 (-)NCBIGRCr8
mRatBN7.23118,396,987 - 118,399,780 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3118,388,546 - 118,400,470 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3122,291,319 - 122,294,112 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03130,890,684 - 130,893,477 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03128,547,420 - 128,550,213 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03123,720,888 - 123,723,520 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3123,721,486 - 123,723,524 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03130,219,280 - 130,221,879 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43118,883,667 - 118,886,327 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13118,789,239 - 118,791,848 (-)NCBI
Celera3117,205,145 - 117,207,804 (-)NCBICelera
Cytogenetic Map3q36NCBI
CENPB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38203,783,851 - 3,786,740 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl203,783,851 - 3,786,740 (-)EnsemblGRCh38hg38GRCh38
GRCh37203,764,498 - 3,767,387 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36203,712,498 - 3,715,337 (-)NCBINCBI36Build 36hg18NCBI36
Build 34203,712,499 - 3,715,337NCBI
Celera203,826,368 - 3,829,208 (-)NCBICelera
Cytogenetic Map20p13NCBI
HuRef203,713,053 - 3,715,727 (-)NCBIHuRef
CHM1_1203,764,809 - 3,767,501 (-)NCBICHM1_1
T2T-CHM13v2.0203,814,791 - 3,817,680 (-)NCBIT2T-CHM13v2.0
Cenpb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392131,019,209 - 131,021,974 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2131,017,102 - 131,021,987 (-)EnsemblGRCm39 Ensembl
GRCm382131,177,289 - 131,180,067 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2131,175,182 - 131,180,067 (-)EnsemblGRCm38mm10GRCm38
MGSCv372131,003,025 - 131,005,748 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362130,868,730 - 130,871,453 (-)NCBIMGSCv36mm8
Celera2132,401,362 - 132,403,874 (-)NCBICelera
Cytogenetic Map2F1NCBI
cM Map263.29NCBI
Cenpb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541514,626,949 - 14,628,748 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541514,626,154 - 14,628,749 (-)NCBIChiLan1.0ChiLan1.0
CENPB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2214,746,002 - 4,748,894 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1204,742,827 - 4,745,719 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0203,864,902 - 3,867,790 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1203,621,694 - 3,624,329 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl203,622,529 - 3,624,329 (-)Ensemblpanpan1.1panPan2
CENPB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12417,569,440 - 17,572,311 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2417,569,663 - 17,572,127 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2417,399,334 - 17,402,018 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02417,988,439 - 17,991,123 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2417,987,999 - 17,990,293 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12417,583,294 - 17,585,978 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02417,694,387 - 17,697,072 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02418,022,036 - 18,024,720 (+)NCBIUU_Cfam_GSD_1.0
Cenpb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640166,483,280 - 166,485,901 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648514,914,644 - 14,916,458 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648514,914,644 - 14,917,265 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CENPB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1731,929,892 - 31,931,712 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11731,929,846 - 31,932,539 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21736,262,448 - 36,264,712 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CENPB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1234,469,577 - 34,472,261 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl234,470,410 - 34,472,221 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660719,981,154 - 9,984,050 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cenpb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247414,869,248 - 4,870,897 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247414,868,453 - 4,870,933 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cenpb
2 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:82
Interacting mature miRNAs:87
Transcripts:ENSRNOT00000002929
Prediction methods:Miranda, Rnahybrid
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
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)384091273129091273Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)391797474136797474Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)389772419134772419Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3115638168135181505Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3112287552135181505Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)395735366140735366Rat


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: ENSRNOT00000080351   ⟹   ENSRNOP00000075557
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3118,388,546 - 118,400,470 (-)Ensembl
Rnor_6.0 Ensembl3123,721,486 - 123,723,524 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000103168   ⟹   ENSRNOP00000093208
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3118,388,546 - 118,400,470 (-)Ensembl
RefSeq Acc Id: NM_001399319   ⟹   NP_001386248
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83138,850,003 - 138,852,796 (-)NCBI
mRatBN7.23118,396,987 - 118,399,780 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001386248 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000075557.2
  ENSRNOP00000093208.1
Ensembl Acc Id: ENSRNOP00000075557   ⟸   ENSRNOT00000080351
Ensembl Acc Id: ENSRNOP00000093208   ⟸   ENSRNOT00000103168
RefSeq Acc Id: NP_001386248   ⟸   NM_001399319
Protein Domains
HTH CENPB-type   HTH psq-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2KAW9-F1-model_v2 AlphaFold A0A0G2KAW9 1-603 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304794 AgrOrtholog
BioCyc Gene G2FUF-47821 BioCyc
Ensembl Genes ENSRNOG00000057284 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000080351.2 UniProtKB/TrEMBL
  ENSRNOT00000103168.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.1090 UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
InterPro CenT-Element_Derived UniProtKB/TrEMBL
  Centromere_CenpB_dimerisation UniProtKB/TrEMBL
  DDE_SF_endonuclease_CENPB-like UniProtKB/TrEMBL
  Dimerisation_CENP-B UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  HTH_Psq UniProtKB/TrEMBL
  Pogo/CenpB/PDC2_DNA-bd_HTH UniProtKB/TrEMBL
NCBI Gene 362217 ENTREZGENE
PANTHER MAJOR CENTROMERE AUTOANTIGEN B UniProtKB/TrEMBL
  TRANSPOSON UniProtKB/TrEMBL
Pfam Cenp-B_dimeris UniProtKB/TrEMBL
  CENP-B_N UniProtKB/TrEMBL
  DDE UniProtKB/TrEMBL
  Transposase_Tc5 UniProtKB/TrEMBL
PhenoGen Cenpb PhenoGen
PROSITE HTH_CENPB UniProtKB/TrEMBL
  HTH_PSQ UniProtKB/TrEMBL
RatGTEx ENSRNOG00000057284 RatGTEx
SMART CENPB UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
  SSF101160 UniProtKB/TrEMBL
UniProt A0A0G2KAW9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-03 Cenpb  centromere protein B  Cenpb_predicted  centromere autoantigen B (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Cenpb_predicted  centromere autoantigen B (predicted)      Symbol and Name status set to approved 70820 APPROVED