Ccni (cyclin I) - Rat Genome Database

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Gene: Ccni (cyclin I) Rattus norvegicus
Analyze
Symbol: Ccni
Name: cyclin I
RGD ID: 1309209
Description: Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Predicted to be involved in G1/S transition of mitotic cell cycle. Predicted to be part of cyclin-dependent protein kinase holoenzyme complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human CCNI (cyclin I); INTERACTS WITH 6-propyl-2-thiouracil; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cyclin-I; LOC289500
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81415,164,047 - 15,186,885 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1415,164,095 - 15,186,885 (+)EnsemblGRCr8
mRatBN7.21414,879,698 - 14,902,510 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1414,879,717 - 14,902,510 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1414,888,988 - 14,911,658 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01416,208,004 - 16,230,674 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01414,903,257 - 14,925,929 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01416,341,510 - 16,364,326 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1416,341,536 - 16,364,326 (+)Ensemblrn6Rnor6.0
Rnor_5.01416,267,506 - 16,290,318 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41416,437,340 - 16,460,130 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1414,282,201 - 14,304,991 (+)NCBICelera
RGSC_v3.11416,437,274 - 16,460,127 (+)NCBI
Cytogenetic Map14p22NCBI
JBrowse:




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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Ccni
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81415,164,047 - 15,186,885 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1415,164,095 - 15,186,885 (+)EnsemblGRCr8
mRatBN7.21414,879,698 - 14,902,510 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1414,879,717 - 14,902,510 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1414,888,988 - 14,911,658 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01416,208,004 - 16,230,674 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01414,903,257 - 14,925,929 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01416,341,510 - 16,364,326 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1416,341,536 - 16,364,326 (+)Ensemblrn6Rnor6.0
Rnor_5.01416,267,506 - 16,290,318 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41416,437,340 - 16,460,130 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1414,282,201 - 14,304,991 (+)NCBICelera
RGSC_v3.11416,437,274 - 16,460,127 (+)NCBI
Cytogenetic Map14p22NCBI
CCNI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38477,047,155 - 77,075,989 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl477,047,155 - 77,076,319 (-)Ensemblhg38GRCh38
GRCh37477,968,308 - 77,997,142 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36478,188,189 - 78,216,149 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34478,326,353 - 78,354,304NCBI
Celera475,270,553 - 75,298,504 (-)NCBICelera
Cytogenetic Map4q21.1NCBI
HuRef473,720,994 - 73,748,951 (-)NCBIHuRef
CHM1_1477,946,423 - 77,974,382 (-)NCBICHM1_1
T2T-CHM13v2.0480,387,967 - 80,416,780 (-)NCBIT2T-CHM13v2.0
Ccni
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39593,329,796 - 93,354,348 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl593,329,792 - 93,354,354 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38593,181,933 - 93,206,495 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl593,181,933 - 93,206,495 (-)Ensemblmm10GRCm38
MGSCv37593,610,959 - 93,635,521 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36594,257,141 - 94,281,232 (-)NCBIMGSCv36mm8
Celera591,335,519 - 91,360,075 (-)NCBICelera
Cytogenetic Map5E2NCBI
cM Map547.29NCBI
Ccni
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554331,698,568 - 1,735,196 (-)Ensembl
ChiLan1.0NW_0049554331,698,568 - 1,735,196 (-)NCBIChiLan1.0ChiLan1.0
CCNI
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2352,986,685 - 53,022,812 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1453,182,420 - 53,215,473 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0447,129,542 - 47,158,419 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1452,968,082 - 52,996,932 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl452,968,082 - 52,996,932 (+)EnsemblpanPan2panpan1.1
CCNI
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1321,612,590 - 1,650,661 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl321,608,330 - 1,645,352 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3240,236,220 - 40,274,002 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0321,642,080 - 1,680,282 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl321,637,827 - 1,680,282 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1321,634,137 - 1,672,319 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0321,589,677 - 1,627,852 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03238,547,915 - 38,585,702 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Ccni
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528510,538,770 - 10,559,788 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936676947,455 - 969,573 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936676947,455 - 968,479 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCNI
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl872,686,106 - 72,719,065 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1872,686,095 - 72,719,307 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2876,887,178 - 76,919,644 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCNI
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1725,547,692 - 25,576,412 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660373,901,103 - 3,931,303 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccni
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475713,887,997 - 13,927,712 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Ccni
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1115,984,633 - 6,007,482 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Ccni
121 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:227
Count of miRNA genes:157
Interacting mature miRNAs:187
Transcripts:ENSRNOT00000002924
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14395787821572472Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14395787818558812Rat
7411573Bw139Body weight QTL 1394.70.001body mass (VT:0001259)body weight gain (CMO:0000420)14140068101Rat
9589814Gluco67Glucose level QTL 674.540.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14140068101Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14939329839411170Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141133490630674469Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141133471628389666Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14395787831121464Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)14117877928Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14862139853621398Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14395787824886169Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1411334716100078267Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141415516Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14131893212Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14862139853621398Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141513759431238250Rat

Markers in Region
BF399292  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21414,899,828 - 14,900,020 (+)MAPPERmRatBN7.2
Rnor_6.01416,361,645 - 16,361,836NCBIRnor6.0
Rnor_5.01416,287,637 - 16,287,828UniSTSRnor5.0
RGSC_v3.41416,457,449 - 16,457,640UniSTSRGSC3.4
Celera1414,302,310 - 14,302,501UniSTS
RH 3.4 Map14173.2UniSTS
Cytogenetic Map14p22UniSTS
RH142357  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21414,902,014 - 14,902,213 (+)MAPPERmRatBN7.2
Rnor_6.01416,363,831 - 16,364,029NCBIRnor6.0
Rnor_5.01416,289,823 - 16,290,021UniSTSRnor5.0
RGSC_v3.41416,459,635 - 16,459,833UniSTSRGSC3.4
Celera1414,304,496 - 14,304,694UniSTS
RH 3.4 Map14175.9UniSTS
Cytogenetic Map14p22UniSTS
AW534411  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21414,885,906 - 14,886,056 (+)MAPPERmRatBN7.2
Rnor_6.01416,347,726 - 16,347,875NCBIRnor6.0
Rnor_5.01416,273,718 - 16,273,867UniSTSRnor5.0
RGSC_v3.41416,443,530 - 16,443,679UniSTSRGSC3.4
Celera1414,288,391 - 14,288,540UniSTS
RH 3.4 Map14172.5UniSTS
Cytogenetic Map14p22UniSTS
RH137017  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21414,902,299 - 14,902,484 (+)MAPPERmRatBN7.2
Rnor_6.01416,364,116 - 16,364,300NCBIRnor6.0
Rnor_5.01416,290,108 - 16,290,292UniSTSRnor5.0
RGSC_v3.41416,459,920 - 16,460,104UniSTSRGSC3.4
Celera1414,304,781 - 14,304,965UniSTS
RH 3.4 Map14174.8UniSTS
Cytogenetic Map14p22UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000002924   ⟹   ENSRNOP00000002924
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1415,164,095 - 15,186,885 (+)Ensembl
mRatBN7.2 Ensembl1414,879,717 - 14,902,510 (+)Ensembl
Rnor_6.0 Ensembl1416,341,536 - 16,364,326 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000137202   ⟹   ENSRNOP00000105637
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1415,168,454 - 15,186,885 (+)Ensembl
RefSeq Acc Id: NM_001105998   ⟹   NP_001099468
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81415,164,095 - 15,186,885 (+)NCBI
mRatBN7.21414,879,717 - 14,902,510 (+)NCBI
Rnor_6.01416,341,536 - 16,364,326 (+)NCBI
Rnor_5.01416,267,506 - 16,290,318 (+)NCBI
RGSC_v3.41416,437,340 - 16,460,130 (+)RGD
Celera1414,282,201 - 14,304,991 (+)RGD
Sequence:
RefSeq Acc Id: XM_006250715   ⟹   XP_006250777
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81415,164,047 - 15,186,884 (+)NCBI
mRatBN7.21414,879,698 - 14,902,509 (+)NCBI
Rnor_6.01416,341,510 - 16,364,325 (+)NCBI
Rnor_5.01416,267,506 - 16,290,318 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063272900   ⟹   XP_063128970
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81415,164,047 - 15,186,884 (+)NCBI
RefSeq Acc Id: NP_001099468   ⟸   NM_001105998
- UniProtKB: D4A5E4 (UniProtKB/TrEMBL),   A6KK51 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250777   ⟸   XM_006250715
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000002924   ⟸   ENSRNOT00000002924
RefSeq Acc Id: XP_063128970   ⟸   XM_063272900
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000105637   ⟸   ENSRNOT00000137202
Protein Domains
Cyclin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A5E4-F1-model_v2 AlphaFold D4A5E4 1-377 view protein structure

Transcriptome

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

Promoters
RGD ID:13699206
Promoter ID:EPDNEW_R9731
Type:multiple initiation site
Name:Ccni_1
Description:cyclin I
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_6.01416,341,531 - 16,341,591EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309209 AgrOrtholog
BioCyc Gene G2FUF-16282 BioCyc
Ensembl Genes ENSRNOG00000002125 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002924 ENTREZGENE
  ENSRNOT00000002924.7 UniProtKB/TrEMBL
  ENSRNOT00000137202 ENTREZGENE
  ENSRNOT00000137202.1 UniProtKB/TrEMBL
Gene3D-CATH Cyclin-like UniProtKB/TrEMBL
InterPro Cyclin UniProtKB/TrEMBL
  Cyclin-like_sf UniProtKB/TrEMBL
  Cyclin_N UniProtKB/TrEMBL
  Cyclin_related UniProtKB/TrEMBL
KEGG Report rno:289500 UniProtKB/TrEMBL
NCBI Gene 289500 ENTREZGENE
PANTHER PTHR10177 UniProtKB/TrEMBL
Pfam Cyclin_N UniProtKB/TrEMBL
PhenoGen Ccni PhenoGen
RatGTEx ENSRNOG00000002125 RatGTEx
SMART CYCLIN UniProtKB/TrEMBL
Superfamily-SCOP Cyclin_like UniProtKB/TrEMBL
UniProt A0ABK0LXM2_RAT UniProtKB/TrEMBL
  A6KK51 ENTREZGENE, UniProtKB/TrEMBL
  D4A5E4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Ccni  cyclin I   Ccni_predicted  cyclin I (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ccni_predicted  cyclin I (predicted)      Symbol and Name status set to approved 70820 APPROVED