Ccnh (cyclin H) - Rat Genome Database

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Gene: Ccnh (cyclin H) Rattus norvegicus
Analyze
Symbol: Ccnh
Name: cyclin H
RGD ID: 69419
Description: Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity and kinase activity. Predicted to contribute to RNA polymerase II general transcription initiation factor activity. Predicted to be involved in several processes, including protein stabilization; regulation of cell cycle process; and regulation of cyclin-dependent protein serine/threonine kinase activity. Predicted to be located in cytoplasm; germ cell nucleus; and nucleoplasm. Predicted to be part of nucleus. Predicted to be active in nucleus. Biomarker of transient cerebral ischemia. Orthologous to human CCNH (cyclin H); PARTICIPATES IN RNA polymerase II transcription initiation pathway; cell cycle pathway, mitotic; nucleotide excision repair pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cyclin-H
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
mRatBN7.2215,834,833 - 15,855,643 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl215,834,833 - 15,855,819 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx222,936,030 - 22,956,622 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0221,036,283 - 21,056,875 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0215,710,083 - 15,730,675 (+)NCBIRnor_WKY
Rnor_6.0213,593,100 - 13,613,910 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl213,593,100 - 13,613,910 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0213,446,659 - 13,467,469 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4214,179,894 - 14,200,704 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1214,100,262 - 14,121,073 (+)NCBI
Celera212,100,804 - 12,121,614 (+)NCBICelera
Cytogenetic Map2q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. A history of TFIIH: two decades of molecular biology on a pivotal transcription/repair factor. Egly JM and Coin F, DNA Repair (Amst). 2011 Jul 15;10(7):714-21. doi: 10.1016/j.dnarep.2011.04.021. Epub 2011 May 17.
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. Molecular cloning of a cell cycle regulation gene cyclin H from ischemic rat brain: expression in neurons after global cerebral ischemia. Jin K, etal., J Neurochem 1999 Oct;73(4):1598-608.
5. Analysis of candidate genes included in the mammary cancer susceptibility 1 (Mcs1) region. Laes JF, etal., Mamm Genome 2001 Mar;12(3):199-206.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
9. Allelic imbalance and altered expression of genes in chromosome 2q11-2q16 from rat mammary gland carcinomas induced by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine. Qiu C, etal., Oncogene. 2003 Feb 27;22(8):1253-60.
10. GOA pipeline RGD automated data pipeline
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Comprehensive gene review and curation RGD comprehensive gene curation
14. 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.
15. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
16. Temporal and spatial expression of cyclin H in rat spinal cord injury. Wu G, etal., Neuromolecular Med. 2011 Sep;13(3):187-96. doi: 10.1007/s12017-011-8150-1. Epub 2011 Jun 28.
Additional References at PubMed
PMID:8692841   PMID:8692842   PMID:9852112   PMID:11319144   PMID:15489334   PMID:21778139   PMID:23393140   PMID:24855060  


Genomics

Comparative Map Data
Ccnh
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2215,834,833 - 15,855,643 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl215,834,833 - 15,855,819 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx222,936,030 - 22,956,622 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0221,036,283 - 21,056,875 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0215,710,083 - 15,730,675 (+)NCBIRnor_WKY
Rnor_6.0213,593,100 - 13,613,910 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl213,593,100 - 13,613,910 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0213,446,659 - 13,467,469 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4214,179,894 - 14,200,704 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1214,100,262 - 14,121,073 (+)NCBI
Celera212,100,804 - 12,121,614 (+)NCBICelera
Cytogenetic Map2q11NCBI
CCNH
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38587,311,471 - 87,412,930 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl587,318,416 - 87,412,930 (-)EnsemblGRCh38hg38GRCh38
GRCh37586,607,288 - 86,708,747 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36586,725,838 - 86,744,592 (-)NCBINCBI36Build 36hg18NCBI36
Build 34586,725,838 - 86,744,592NCBI
Celera582,582,332 - 82,601,086 (-)NCBICelera
Cytogenetic Map5q14.3NCBI
HuRef581,894,247 - 81,913,020 (-)NCBIHuRef
CHM1_1586,123,107 - 86,141,878 (-)NCBICHM1_1
T2T-CHM13v2.0587,792,576 - 87,894,036 (-)NCBIT2T-CHM13v2.0
Ccnh
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391385,337,504 - 85,361,850 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1385,337,527 - 85,371,588 (+)EnsemblGRCm39 Ensembl
GRCm381385,189,377 - 85,213,731 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1385,189,408 - 85,223,469 (+)EnsemblGRCm38mm10GRCm38
MGSCv371385,329,082 - 85,353,328 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361385,662,587 - 85,686,833 (+)NCBIMGSCv36mm8
Celera1387,421,607 - 87,445,967 (+)NCBICelera
Cytogenetic Map13C3NCBI
Ccnh
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541823,790,001 - 23,807,702 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541823,790,398 - 23,807,509 (+)NCBIChiLan1.0ChiLan1.0
CCNH
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1528,094,064 - 28,131,166 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl528,094,064 - 28,116,149 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0527,958,859 - 27,995,815 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CCNH
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1321,046,477 - 21,067,305 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl321,046,472 - 21,178,315 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha322,412,153 - 22,431,889 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0320,955,126 - 20,974,862 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl320,955,145 - 20,976,993 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1320,926,297 - 20,945,993 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0320,888,786 - 20,908,786 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0321,180,551 - 21,200,143 (+)NCBIUU_Cfam_GSD_1.0
Ccnh
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213176,673,557 - 176,690,580 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364695,935,131 - 5,952,460 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364695,933,163 - 5,952,190 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCNH
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl294,980,941 - 95,018,634 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1294,980,938 - 95,019,053 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2297,505,024 - 97,539,020 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCNH
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1481,373,812 - 81,392,454 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl481,373,994 - 81,392,326 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604930,376,461 - 30,412,792 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccnh
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247436,883,114 - 6,902,745 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247436,883,124 - 6,902,518 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccnh
143 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:85
Count of miRNA genes:74
Interacting mature miRNAs:79
Transcripts:ENSRNOT00000049423
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
61368Mcs1Mammary carcinoma susceptibility QTL 14.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777223319447Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat

Markers in Region
RH130655  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2215,848,481 - 15,848,674 (+)MAPPERmRatBN7.2
Rnor_6.0213,606,749 - 13,606,941NCBIRnor6.0
Rnor_5.0213,460,308 - 13,460,500UniSTSRnor5.0
RGSC_v3.4214,193,543 - 14,193,735UniSTSRGSC3.4
Celera212,114,453 - 12,114,645UniSTS
Cytogenetic Map2q12-q14UniSTS
RH141924  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2215,851,030 - 15,851,210 (+)MAPPERmRatBN7.2
Rnor_6.0213,609,298 - 13,609,477NCBIRnor6.0
Rnor_5.0213,462,857 - 13,463,036UniSTSRnor5.0
RGSC_v3.4214,196,092 - 14,196,271UniSTSRGSC3.4
Celera212,117,002 - 12,117,181UniSTS
Cytogenetic Map2q12-q14UniSTS


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 43 57 41 19 41 8 10 74 35 39 11 8
Low 1 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000049423   ⟹   ENSRNOP00000039039
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl215,834,833 - 15,855,643 (+)Ensembl
Rnor_6.0 Ensembl213,593,100 - 13,613,910 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000118807   ⟹   ENSRNOP00000084834
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl215,834,833 - 15,855,819 (+)Ensembl
RefSeq Acc Id: NM_052981   ⟹   NP_443213
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2215,834,833 - 15,855,643 (+)NCBI
Rnor_6.0213,593,100 - 13,613,910 (+)NCBI
Rnor_5.0213,446,659 - 13,467,469 (+)NCBI
RGSC_v3.4214,179,894 - 14,200,704 (+)RGD
Celera212,100,804 - 12,121,614 (+)RGD
Sequence:
RefSeq Acc Id: XM_039103265   ⟹   XP_038959193
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2215,835,065 - 15,854,084 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_443213   ⟸   NM_052981
- UniProtKB: Q99JE5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000039039   ⟸   ENSRNOT00000049423
RefSeq Acc Id: XP_038959193   ⟸   XM_039103265
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000084834   ⟸   ENSRNOT00000118807
Protein Domains
CYCLIN

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9R1A0-F1-model_v2 AlphaFold Q9R1A0 1-323 view protein structure

Transcriptome

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

Promoters
RGD ID:13691049
Promoter ID:EPDNEW_R1574
Type:initiation region
Name:Ccnh_1
Description:cyclin H
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_6.0213,593,387 - 13,593,447EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69419 AgrOrtholog
BioCyc Gene G2FUF-54931 BioCyc
Ensembl Genes ENSRNOG00000031656 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000039039 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000084834.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000049423 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000118807.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6886953 IMAGE-MGC_LOAD
InterPro Cyclin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin/Ssn8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CyclinH/Ccl1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84389 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72647 IMAGE-MGC_LOAD
NCBI Gene 84389 ENTREZGENE
PANTHER PTHR10026 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cyclin_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cyclin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ccnh PhenoGen
SMART CYCLIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47954 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC231118
TIGRFAMs ccl1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6A2R2_RAT UniProtKB/TrEMBL
  CCNH_RAT UniProtKB/Swiss-Prot
  Q99JE5 ENTREZGENE
  Q9R1A0 ENTREZGENE
UniProt Secondary Q99JE5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2002-06-10 Ccnh  cyclin H      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in normal postmitotic neurons 69371
gene_process controls cell cycle 68725
gene_process controls cell cycle 69371
gene_regulation expression is increased in surviving neurons that are ischemic 69371