Ccnb3 (cyclin B3) - Rat Genome Database

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Gene: Ccnb3 (cyclin B3) Rattus norvegicus
Analyze
Symbol: Ccnb3
Name: cyclin B3
RGD ID: 1564367
Description: Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Predicted to be involved in mitotic cell cycle phase transition. Predicted to be located in nuclear speck. Predicted to be part of cyclin-dependent protein kinase holoenzyme complex. Predicted to be active in centrosome; cytoplasm; and nucleus. Orthologous to human CCNB3 (cyclin B3); PARTICIPATES IN cell cycle pathway, mitotic; p53 signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: G2/mitotic-specific cyclin-B3; LOC317389; RGD1564367; similar to cyclin B3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
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
mRatBN7.2X15,478,050 - 15,543,292 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX15,478,065 - 15,542,885 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX20,294,337 - 20,358,758 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X19,724,545 - 19,788,967 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X15,989,504 - 16,053,924 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X16,300,752 - 16,402,206 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX16,337,102 - 16,402,202 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X17,122,155 - 17,187,194 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X27,565,661 - 27,623,293 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX15,515,387 - 15,617,162 (+)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Ccnb3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X15,478,050 - 15,543,292 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX15,478,065 - 15,542,885 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX20,294,337 - 20,358,758 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X19,724,545 - 19,788,967 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X15,989,504 - 16,053,924 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X16,300,752 - 16,402,206 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX16,337,102 - 16,402,202 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X17,122,155 - 17,187,194 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X27,565,661 - 27,623,293 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX15,515,387 - 15,617,162 (+)NCBICelera
Cytogenetic MapXq12NCBI
CCNB3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X50,202,713 - 50,351,914 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX50,202,713 - 50,351,914 (+)EnsemblGRCh38hg38GRCh38
GRCh37X49,969,416 - 50,094,913 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X50,044,280 - 50,111,653 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X49,860,575 - 49,927,945NCBI
CeleraX54,071,225 - 54,138,495 (+)NCBICelera
Cytogenetic MapXp11.22NCBI
HuRefX47,471,841 - 47,539,060 (+)NCBIHuRef
CHM1_1X50,107,188 - 50,174,744 (+)NCBICHM1_1
T2T-CHM13v2.0X49,520,371 - 49,623,348 (+)NCBIT2T-CHM13v2.0
Ccnb3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X6,845,890 - 6,907,894 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX6,845,891 - 6,907,858 (-)EnsemblGRCm39 Ensembl
GRCm38X6,979,652 - 7,041,635 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX6,979,652 - 7,041,619 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X6,556,778 - 6,618,745 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X6,136,611 - 6,198,578 (-)NCBIMGSCv36mm8
CeleraX4,421,565 - 4,483,832 (+)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX3.13NCBI
Ccnb3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555431,377,932 - 1,444,327 (+)NCBIChiLan1.0ChiLan1.0
CCNB3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1X51,626,146 - 51,728,152 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X42,409,954 - 42,511,811 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X50,157,122 - 50,223,759 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX50,157,122 - 50,223,547 (+)Ensemblpanpan1.1panPan2
CCNB3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X42,951,030 - 43,041,616 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX42,949,558 - 43,012,122 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX17,340,549 - 17,389,577 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X43,102,335 - 43,180,933 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX43,088,724 - 43,151,391 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X43,088,178 - 43,137,193 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X43,075,470 - 43,124,516 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X43,170,367 - 43,219,386 (+)NCBIUU_Cfam_GSD_1.0
Ccnb3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X35,485,077 - 35,542,195 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049367211,729,979 - 1,782,399 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCNB3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX43,922,804 - 43,990,929 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X43,922,729 - 43,988,939 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X48,849,863 - 48,916,024 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCNB3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X47,059,747 - 47,142,911 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX47,085,605 - 47,142,788 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666086642,635 - 731,855 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccnb3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248931,788,915 - 1,862,015 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248931,775,726 - 1,861,925 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccnb3
199 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:34
Count of miRNA genes:33
Interacting mature miRNAs:34
Transcripts:ENSRNOT00000003954
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
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X144797220991088Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X162371522646544Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat


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

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 11
Low 6 4 8 19
Below cutoff 16 21 10 8 10 5 5 38 23 10 3 5

Sequence


RefSeq Acc Id: ENSRNOT00000003954   ⟹   ENSRNOP00000003954
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX15,478,065 - 15,542,885 (+)Ensembl
Rnor_6.0 EnsemblX16,337,102 - 16,402,202 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000094271   ⟹   ENSRNOP00000093786
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX15,478,065 - 15,542,837 (+)Ensembl
RefSeq Acc Id: NM_001401153   ⟹   NP_001388082
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X15,478,050 - 15,542,938 (+)NCBI
RefSeq Acc Id: XM_039100299   ⟹   XP_038956227
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X15,478,050 - 15,543,292 (+)NCBI
RefSeq Acc Id: XM_039100300   ⟹   XP_038956228
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X15,478,066 - 15,543,292 (+)NCBI
RefSeq Acc Id: XR_005498305
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X15,478,050 - 15,531,874 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001388082 (Get FASTA)   NCBI Sequence Viewer  
  XP_038956227 (Get FASTA)   NCBI Sequence Viewer  
  XP_038956228 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ADX01544 (Get FASTA)   NCBI Sequence Viewer  
  EDL83865 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003954
  ENSRNOP00000003954.6
  ENSRNOP00000093786.1
RefSeq Acc Id: ENSRNOP00000003954   ⟸   ENSRNOT00000003954
RefSeq Acc Id: XP_038956227   ⟸   XM_039100299
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AMG1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038956228   ⟸   XM_039100300
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AMG1 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000093786   ⟸   ENSRNOT00000094271
RefSeq Acc Id: NP_001388082   ⟸   NM_001401153
- UniProtKB: K7NAQ4 (UniProtKB/TrEMBL),   F1LVT0 (UniProtKB/TrEMBL),   A0A8I6AMG1 (UniProtKB/TrEMBL)
Protein Domains
Cyclin C-terminal   Cyclin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LVT0-F1-model_v2 AlphaFold F1LVT0 1-1404 view protein structure

Transcriptome

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

Promoters
RGD ID:13701757
Promoter ID:EPDNEW_R12277
Type:single initiation site
Name:Ccnb3_1
Description:cyclin B3
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_6.0X16,337,090 - 16,337,150EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564367 AgrOrtholog
BioCyc Gene G2FUF-2875 BioCyc
Ensembl Genes ENSRNOG00000002951 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003954 ENTREZGENE
  ENSRNOT00000003954.7 UniProtKB/TrEMBL
  ENSRNOT00000094271.1 UniProtKB/TrEMBL
Gene3D-CATH Cyclin-like UniProtKB/TrEMBL
InterPro Cyclin UniProtKB/TrEMBL
  Cyclin-like UniProtKB/TrEMBL
  Cyclin-like_sf UniProtKB/TrEMBL
  Cyclin_C UniProtKB/TrEMBL
  Cyclin_N UniProtKB/TrEMBL
  Cyclins_cyclin-box UniProtKB/TrEMBL
KEGG Report rno:317389 UniProtKB/TrEMBL
NCBI Gene 317389 ENTREZGENE
PANTHER PTHR10177 UniProtKB/TrEMBL
  PTHR10177:SF214 UniProtKB/TrEMBL
Pfam Cyclin_C UniProtKB/TrEMBL
  Cyclin_N UniProtKB/TrEMBL
PhenoGen Ccnb3 PhenoGen
PROSITE CYCLINS UniProtKB/TrEMBL
RatGTEx ENSRNOG00000002951 RatGTEx
SMART CYCLIN UniProtKB/TrEMBL
  Cyclin_C UniProtKB/TrEMBL
Superfamily-SCOP Cyclin_like UniProtKB/TrEMBL
UniProt A0A8I6AMG1 ENTREZGENE, UniProtKB/TrEMBL
  F1LVT0 ENTREZGENE, UniProtKB/TrEMBL
  K7NAQ4 ENTREZGENE
UniProt Secondary K7NAQ4 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ccnb3  cyclin B3   Ccnb3_predicted  cyclin B3 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Ccnb3_predicted  cyclin B3 (predicted)  RGD1564367_predicted  similar to cyclin B3 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1564367_predicted  similar to cyclin B3 (predicted)  LOC317389  similar to cyclin B3  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317389  similar to cyclin B3      Symbol and Name status set to provisional 70820 PROVISIONAL