Cdt1 (chromatin licensing and DNA replication factor 1) - Rat Genome Database

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Gene: Cdt1 (chromatin licensing and DNA replication factor 1) Rattus norvegicus
Analyze
Symbol: Cdt1
Name: chromatin licensing and DNA replication factor 1
RGD ID: 1309211
Description: Predicted to enable DNA binding activity; DNA polymerase binding activity; and chromatin binding activity. Predicted to be involved in several processes, including DNA replication checkpoint signaling; attachment of mitotic spindle microtubules to kinetochore; and regulation of DNA-templated DNA replication. Predicted to act upstream of or within regulation of nuclear cell cycle DNA replication. Predicted to be located in kinetochore and nuclear body. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Meier-Gorlin syndrome 4. Orthologous to human CDT1 (chromatin licensing and DNA replication factor 1); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: DNA replication factor Cdt1; LOC292071; retroviral integration site 2; Ris2
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
mRatBN7.21950,620,713 - 50,625,659 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1950,620,713 - 50,625,659 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1957,415,480 - 57,420,429 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01958,095,635 - 58,100,581 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01960,314,104 - 60,319,053 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01955,381,565 - 55,386,511 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1955,381,565 - 55,386,511 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01966,090,081 - 66,095,027 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41952,848,559 - 52,853,880 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11952,852,915 - 52,858,234 (+)NCBI
Celera1949,860,119 - 49,865,065 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-diaminotoluene  (ISO)
2-methylcholine  (ISO)
3-methylcholanthrene  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
antimycin A  (ISO)
aristolochic acid A  (ISO)
atrazine  (ISO)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
bromobenzene  (EXP)
C60 fullerene  (EXP)
caffeine  (ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
chromium(6+)  (ISO)
cisplatin  (ISO)
cobalt dichloride  (EXP)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
cyclosporin A  (ISO)
deguelin  (ISO)
diazinon  (EXP)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (ISO)
diclofenac  (ISO)
dorsomorphin  (ISO)
endosulfan  (EXP)
Enterolactone  (ISO)
ethyl methanesulfonate  (ISO)
fenthion  (ISO)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
glycidol  (EXP)
Lasiocarpine  (ISO)
lidocaine  (EXP)
menadione  (ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
N-(6-acetamidohexyl)acetamide  (ISO)
N-nitrosodiethylamine  (ISO)
nickel atom  (ISO)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
nitrofen  (EXP)
nocodazole  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
palbociclib  (ISO)
paracetamol  (EXP,ISO)
PCB138  (ISO)
pevonedistat  (ISO)
phenethyl isothiocyanate  (ISO)
phenobarbital  (ISO)
phenylmercury acetate  (ISO)
phytoestrogen  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
propanal  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
simvastatin  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sunitinib  (ISO)
tebufenpyrad  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
troglitazone  (ISO)
valproic acid  (ISO)
vancomycin  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
kinetochore  (ISO)
nuclear body  (IEA,ISO)
nucleoplasm  (ISO)
nucleus  (IBA,ISO)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
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:11125146   PMID:11850834   PMID:12192004   PMID:14672932   PMID:14993212   PMID:21856198   PMID:22581055   PMID:24217620   PMID:26842564  


Genomics

Comparative Map Data
Cdt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21950,620,713 - 50,625,659 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1950,620,713 - 50,625,659 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1957,415,480 - 57,420,429 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01958,095,635 - 58,100,581 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01960,314,104 - 60,319,053 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01955,381,565 - 55,386,511 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1955,381,565 - 55,386,511 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01966,090,081 - 66,095,027 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41952,848,559 - 52,853,880 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11952,852,915 - 52,858,234 (+)NCBI
Celera1949,860,119 - 49,865,065 (+)NCBICelera
Cytogenetic Map19q12NCBI
CDT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381688,803,789 - 88,809,258 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1688,803,789 - 88,809,258 (+)EnsemblGRCh38hg38GRCh38
GRCh371688,870,197 - 88,875,666 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361687,397,687 - 87,403,167 (+)NCBINCBI36Build 36hg18NCBI36
Celera1673,938,823 - 73,944,303 (+)NCBICelera
Cytogenetic Map16q24.3NCBI
HuRef1674,567,412 - 74,572,892 (+)NCBIHuRef
CHM1_11690,281,453 - 90,286,933 (+)NCBICHM1_1
T2T-CHM13v2.01694,874,309 - 94,879,778 (+)NCBIT2T-CHM13v2.0
Cdt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398123,294,754 - 123,299,869 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8123,294,754 - 123,300,293 (+)EnsemblGRCm39 Ensembl
GRCm388122,568,015 - 122,573,130 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8122,568,015 - 122,573,554 (+)EnsemblGRCm38mm10GRCm38
MGSCv378125,091,915 - 125,097,030 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368125,454,105 - 125,459,220 (+)NCBIMGSCv36mm8
Celera8126,797,613 - 126,802,728 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map871.91NCBI
Cdt1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555412,683,408 - 2,687,102 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555412,683,030 - 2,687,883 (+)NCBIChiLan1.0ChiLan1.0
CDT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan116104,488,752 - 104,494,459 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01669,516,728 - 69,522,419 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11689,173,312 - 89,178,809 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1689,174,071 - 89,177,823 (+)Ensemblpanpan1.1panPan2
CDT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1564,566,035 - 64,570,361 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl564,566,043 - 64,570,748 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha564,577,507 - 64,581,789 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0564,786,263 - 64,790,545 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl564,786,266 - 64,790,971 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1564,812,442 - 64,816,851 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0564,643,948 - 64,648,365 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0565,049,993 - 65,054,410 (-)NCBIUU_Cfam_GSD_1.0
Cdt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934925,163,147 - 25,172,972 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936641917,435 - 920,981 (-)EnsemblSpeTri2.0
SpeTri2.0NW_004936641916,695 - 925,411 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CDT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6893,381 - 897,934 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16893,377 - 897,706 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.261,083,762 - 1,089,922 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CDT1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1574,190,409 - 74,196,589 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl574,190,947 - 74,195,972 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660471,482,389 - 1,488,114 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cdt1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624746809,252 - 812,993 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624746808,463 - 813,464 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cdt1
30 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:65
Count of miRNA genes:56
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000018923
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
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194997648153225766Rat


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 26 29 24 10 24 37 20 26
Low 1 14 23 12 9 12 4 7 33 13 14 11 4
Below cutoff 3 5 5 5 4 4 4 2 1 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018923   ⟹   ENSRNOP00000018923
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1950,620,713 - 50,625,659 (+)Ensembl
Rnor_6.0 Ensembl1955,381,565 - 55,386,511 (+)Ensembl
RefSeq Acc Id: NM_001106192   ⟹   NP_001099662
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21950,620,713 - 50,625,659 (+)NCBI
Rnor_6.01955,381,565 - 55,386,511 (+)NCBI
Rnor_5.01966,090,081 - 66,095,027 (+)NCBI
RGSC_v3.41952,848,559 - 52,853,880 (+)RGD
Celera1949,860,119 - 49,865,065 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099662 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92755 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018923
  ENSRNOP00000018923.4
Reference Protein Sequences
RefSeq Acc Id: NP_001099662   ⟸   NM_001106192
- UniProtKB: D3ZKD4 (UniProtKB/TrEMBL),   A6IZS7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018923   ⟸   ENSRNOT00000018923
Protein Domains
CDT1 Geminin-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZKD4-F1-model_v2 AlphaFold D3ZKD4 1-556 view protein structure

Transcriptome

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

Promoters
RGD ID:13701211
Promoter ID:EPDNEW_R11734
Type:single initiation site
Name:Cdt1_1
Description:chromatin licensing and DNA replication factor 1
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_6.01955,381,593 - 55,381,653EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309211 AgrOrtholog
BioCyc Gene G2FUF-5382 BioCyc
Ensembl Genes ENSRNOG00000013970 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018923 ENTREZGENE
  ENSRNOT00000018923.6 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.1420 UniProtKB/TrEMBL
InterPro Cdt1 UniProtKB/TrEMBL
  Cdt1_C UniProtKB/TrEMBL
  Cdt1_C_WH_dom_sf UniProtKB/TrEMBL
  DNA_replication_fac_CDT1-like UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:292071 UniProtKB/TrEMBL
NCBI Gene 292071 ENTREZGENE
PANTHER DNA REPLICATION FACTOR CDT1 UniProtKB/TrEMBL
  PTHR28637 UniProtKB/TrEMBL
Pfam CDT1 UniProtKB/TrEMBL
  CDT1_C UniProtKB/TrEMBL
PhenoGen Cdt1 PhenoGen
RatGTEx ENSRNOG00000013970 RatGTEx
SMART CDT1 UniProtKB/TrEMBL
Superfamily-SCOP SSF46785 UniProtKB/TrEMBL
UniProt A6IZS7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKD4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Cdt1  chromatin licensing and DNA replication factor 1  Ris2_predicted  retroviral integration site 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Ris2_predicted  retroviral integration site 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED