CCNI

gene
On this page

Also known as CCNI1

Summary

CCNI (cyclin I, HGNC:1595) is a protein-coding gene on chromosome 4q21.1, encoding Cyclin-I (Q14094).

The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. This cyclin shows the highest similarity with cyclin G. The transcript of this gene was found to be expressed constantly during cell cycle progression.

Source: NCBI Gene 10983 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 45 total
  • Druggable target: yes
  • MANE Select transcript: NM_006835

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1595
Approved symbolCCNI
Namecyclin I
Location4q21.1
Locus typegene with protein product
StatusApproved
AliasesCCNI1
Ensembl geneENSG00000118816
Ensembl biotypeprotein_coding
OMIM618783
Entrez10983

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 26 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000237654, ENST00000504697, ENST00000505609, ENST00000506614, ENST00000507788, ENST00000511943, ENST00000513774, ENST00000515468, ENST00000515790, ENST00000718433, ENST00000887836, ENST00000887837, ENST00000887838, ENST00000887839, ENST00000887840, ENST00000887841, ENST00000887842, ENST00000887843, ENST00000887844, ENST00000912006, ENST00000912007, ENST00000912008, ENST00000912009, ENST00000950255, ENST00000950256, ENST00000950257, ENST00000950258, ENST00000950259, ENST00000950260, ENST00000950261

RefSeq mRNA: 10 — MANE Select: NM_006835 NM_001348132, NM_001348133, NM_001348134, NM_001348135, NM_001348136, NM_001348137, NM_001348138, NM_001348139, NM_001348140, NM_006835

CCDS: CCDS3580

Canonical transcript exons

ENST00000237654 — 7 exons

ExonStartEnd
ENSE000010779257704715577048662
ENSE000010779267707547277075989
ENSE000010779297705515077055380
ENSE000034815007705850777058635
ENSE000035790147705624977056323
ENSE000036838847705596277056102
ENSE000040350767706624977066405

Expression profiles

Bgee: expression breadth ubiquitous, 308 present calls, max score 99.85.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 195.2465 / max 2235.3759, expressed in 1826 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter IDTPM avgSamples expressed
52688171.42281826
5268717.30181778
526891.7090919
526851.5138976
526840.6379429
2032540.6333358
2032510.5354290
2032530.4785228
2032560.3585172
2032550.2918118

Top tissues by expression

308 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
paraflocculusUBERON:000535199.85gold quality
cortical plateUBERON:000534399.75gold quality
parotid glandUBERON:000183199.71gold quality
ganglionic eminenceUBERON:000402399.65gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099199.64gold quality
colonic epitheliumUBERON:000039799.61gold quality
postcentral gyrusUBERON:000258199.61gold quality
parietal lobeUBERON:000187299.60gold quality
blood vessel layerUBERON:000479799.60gold quality
Brodmann (1909) area 46UBERON:000648399.57gold quality
caput epididymisUBERON:000435899.55gold quality
superficial temporal arteryUBERON:000161499.51gold quality
cauda epididymisUBERON:000436099.51gold quality
nippleUBERON:000203099.50gold quality
cardia of stomachUBERON:000116299.48gold quality
endometrium epitheliumUBERON:000481199.48gold quality
cartilage tissueUBERON:000241899.47gold quality
adult organismUBERON:000702399.47gold quality
urethraUBERON:000005799.46gold quality
ponsUBERON:000098899.45gold quality
corpus epididymisUBERON:000435999.44gold quality
ventricular zoneUBERON:000305399.43gold quality
orbitofrontal cortexUBERON:000416799.43gold quality
oocyteCL:000002399.39gold quality
pylorusUBERON:000116699.39gold quality
type B pancreatic cellCL:000016999.35gold quality
mammalian vulvaUBERON:000099799.35gold quality
mammary ductUBERON:000176599.35gold quality
frontal poleUBERON:000279599.33gold quality
pericardiumUBERON:000240799.32gold quality

Single-cell (SCXA)

Detected in 25 experiment(s), a significant marker in 13.

ExperimentMarker?Max mean expression
E-MTAB-7316yes3076.73
E-GEOD-124263yes2601.83
E-GEOD-137537yes2229.12
E-HCAD-4yes95.81
E-HCAD-11yes51.68
E-CURD-88yes33.09
E-CURD-122yes32.21
E-GEOD-134144yes31.76
E-MTAB-9543yes20.78
E-CURD-112yes11.14
E-MTAB-10042yes10.07
E-GEOD-125970yes7.38
E-MTAB-7249no6912.64
E-MTAB-9154no2941.00
E-MTAB-10485no2324.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

19 targeting CCNI, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-218-5P99.9372.222103
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-471999.7372.103329
HSA-MIR-4804-3P99.6567.78866
HSA-MIR-7156-5P99.6468.811369
HSA-MIR-7152-5P99.6069.332094
HSA-MIR-6758-3P99.5767.551078
HSA-MIR-186-3P99.5166.241685
HSA-MIR-427399.4567.931206
HSA-MIR-428499.3665.251293
HSA-MIR-133A-3P99.2771.531270
HSA-MIR-133B99.2771.531270
HSA-MIR-149-5P99.2567.161315
HSA-MIR-449B-3P99.2067.241047
HSA-MIR-3074-5P98.8266.561414
HSA-MIR-4680-3P98.6468.602093
HSA-MIR-4720-3P98.5068.88988
HSA-MIR-4662A-5P98.4867.181007

Literature-anchored findings (GeneRIF, showing 4)

  • The increased levels of cyclin I and GDI2 found to be associated with pancreatic carcinoma were further confirmed by Western blot analyses in an independent series of serum samples and/or pancreatic juice samples (PMID:17507299)
  • Knockdown of Cyclin I induced cell cycle arrest at S/G2/M phases. (PMID:23907122)
  • A cyclin I-Cdk5 complex forms a critical antiapoptotic factor in the process of generating cisplatin resistance in cervical cancer. (PMID:26698249)
  • CDK6 is activated by the atypical cyclin I to promote E2F-mediated gene expression and cancer cell proliferation. (PMID:37081792)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
danio_rerioccniENSDARG00000068214
mus_musculusCcniENSMUSG00000063015
rattus_norvegicusCcniENSRNOG00000002125
drosophila_melanogasterCycBFBGN0000405
drosophila_melanogasterCycDFBGN0010315
drosophila_melanogasterCycEFBGN0010382
caenorhabditis_elegansWBGENE00000865
caenorhabditis_elegansWBGENE00000866
caenorhabditis_eleganscyb-2.2WBGENE00000867
caenorhabditis_elegansWBGENE00000870
caenorhabditis_eleganscye-1WBGENE00000871

Paralogs (18): CCNE1 (ENSG00000105173), CCNP (ENSG00000105219), CCNJ (ENSG00000107443), CCND1 (ENSG00000110092), CCND3 (ENSG00000112576), CCNG1 (ENSG00000113328), CCND2 (ENSG00000118971), CCNA1 (ENSG00000133101), CCNB1 (ENSG00000134057), CCNJL (ENSG00000135083), CCNG2 (ENSG00000138764), CCNA2 (ENSG00000145386), CCNB3 (ENSG00000147082), CCNO (ENSG00000152669), CCNB2 (ENSG00000157456), CCNF (ENSG00000162063), CCNE2 (ENSG00000175305), CCNI2 (ENSG00000205089)

Protein

Protein identifiers

Cyclin-IQ14094 (reviewed: Q14094)

All UniProt accessions (6): Q14094, D6RDK3, D6REZ3, D6RG12, D6RH01, H0YA27

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus membrane.

Tissue specificity. Highest levels in adult heart, brain and skeletal muscle. Lower levels in adult placenta, lung, kidney and pancreas. Also high levels in fetal brain and lower levels in fetal lung, liver and kidney. Also abundant in testis and thyroid.

Similarity. Belongs to the cyclin family.

Isoforms (2)

UniProt IDNamesCanonical?
Q14094-11yes
Q14094-22

RefSeq proteins (10): NP_001335061, NP_001335062, NP_001335063, NP_001335064, NP_001335065, NP_001335066, NP_001335067, NP_001335068, NP_001335069, NP_006826* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006671Cyclin_NDomain
IPR013763Cyclin-like_domDomain
IPR036915Cyclin-like_sfHomologous_superfamily
IPR039361CyclinFamily

Pfam: PF00134

UniProt features (8 total): sequence conflict 3, chain 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q14094-F172.930.46

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 266 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, PAX4_01, TGCGCANK_UNKNOWN, ENK_UV_RESPONSE_KERATINOCYTE_UP, GOBP_CELL_CYCLE_PHASE_TRANSITION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, MORF_HDAC1, HSIAO_HOUSEKEEPING_GENES, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_DN, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, GOBP_MALE_GAMETE_GENERATION, WOO_LIVER_CANCER_RECURRENCE_UP, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP

GO Biological Process (2): G1/S transition of mitotic cell cycle (GO:0000082), spermatogenesis (GO:0007283)

GO Molecular Function (2): cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538), protein binding (GO:0005515)

GO Cellular Component (5): cyclin-dependent protein kinase holoenzyme complex (GO:0000307), nucleus (GO:0005634), cytoplasm (GO:0005737), nuclear membrane (GO:0031965), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
mitotic cell cycle1
mitotic cell cycle phase transition1
cell cycle G1/S phase transition1
developmental process involved in reproduction1
male gamete generation1
cyclin-dependent protein serine/threonine kinase activity1
cyclin-dependent protein kinase regulator activity1
binding1
serine/threonine protein kinase complex1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
nucleus1
nuclear envelope1
organelle membrane1

Protein interactions and networks

STRING

1826 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CCNIAZIN1O14977580
CCNICDK5Q00535571
CCNIGRIA2P42262461
CCNIGREB1Q4ZG55461
CCNINEIL1Q96FI4455
CCNICCNL2Q96S94439
CCNICYFIP2Q96F07424
CCNIVCYO14598418
CCNITOR1BO14657418
CCNIFRS2Q8WU20398
CCNIIGFBP7Q16270385
CCNIEPB41L5Q9HCM4385
CCNIKCNA1Q09470379
CCNITMEM63BQ5T3F8378
CCNIGRIA3P42263374

IntAct

24 interactions, top by confidence:

ABTypeScore
CDK5FIBPpsi-mi:“MI:0914”(association)0.840
CDK5CCNIpsi-mi:“MI:0915”(physical association)0.750
CCNICDK5psi-mi:“MI:0915”(physical association)0.750
CDK3CCNIpsi-mi:“MI:0915”(physical association)0.560
CCNIZMYND19psi-mi:“MI:0915”(physical association)0.560
CDK6CCNIpsi-mi:“MI:0915”(physical association)0.560
CDK16CCNIpsi-mi:“MI:0915”(physical association)0.370
CDC25ACCNIpsi-mi:“MI:0915”(physical association)0.370
CCNIIL1RAPpsi-mi:“MI:0915”(physical association)0.370
CCNIKRT18psi-mi:“MI:0915”(physical association)0.370
AKT1CCNIpsi-mi:“MI:0915”(physical association)0.370
CCNICEP63psi-mi:“MI:0915”(physical association)0.000
CEP63CCNIpsi-mi:“MI:0915”(physical association)0.000
CCNICDK6psi-mi:“MI:0915”(physical association)0.000
CCNIZMYND19psi-mi:“MI:0915”(physical association)0.000
cyaCCNIpsi-mi:“MI:0915”(physical association)0.000

BioGRID (22): CCNI (Affinity Capture-RNA), CCNI (Affinity Capture-MS), CCNI (Two-hybrid), CCNI (Two-hybrid), CCNI (Two-hybrid), CDK5 (Two-hybrid), ZMYND19 (Two-hybrid), CDK3 (Two-hybrid), CCNI (Two-hybrid), CCNI (Affinity Capture-RNA), CDK5 (Affinity Capture-MS), CCNI (Negative Genetic), CCNI (Affinity Capture-MS), CCNI (Affinity Capture-MS), CCNI (Affinity Capture-MS)

ESM2 similar proteins: A0A494C0Z2, A0A494C191, A1L3C1, A2RRU4, A4Q9F3, A6NJR5, A6NLX3, A6NNV3, A6QM06, A6QNT4, D4A6L0, E1BBQ2, E9PGG2, O00255, O60320, O88559, P0DTA3, P0DUD1, P0DUD2, P0DUD3, P0DUD4, P0DUX0, P0DUX1, P0DV79, P29590, P40338, P56726, P97260, Q0P5I0, Q12770, Q14094, Q32L49, Q495Y7, Q5IBH6, Q5MJ68, Q5MNU5, Q5Q9Z2, Q5RDC3, Q5T848, Q69Z89

Diamond homologs: O08918, P13351, P24868, P24869, P25011, P25012, P25322, P30183, P30278, P30279, P30280, P39950, P46277, P46278, P51945, P51959, Q04827, Q0JIF2, Q0P5D3, Q14094, Q16589, Q39068, Q39069, Q52QT8, Q5E9I1, Q5R5D0, Q61456, Q6AY13, Q6ZMN8, Q8WNW2, Q92161, Q95TJ9, Q9Z2V9, O01501, O15995, O42575, O48790, O96020, P04962, P0C242

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 12 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
cell division523.1×3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

45 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance31
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

933 predictions. Top by Δscore:

VariantEffectΔscore
4:77055960:A:ACdonor_gain1.0000
4:77055961:C:CCdonor_gain1.0000
4:77058632:CATT:Cacceptor_gain1.0000
4:77066243:CATTA:Cdonor_loss1.0000
4:77066244:ATTAC:Adonor_loss1.0000
4:77066245:TTAC:Tdonor_loss1.0000
4:77066246:TACCT:Tdonor_loss1.0000
4:77066406:CT:Cacceptor_loss1.0000
4:77075485:T:TAdonor_gain1.0000
4:77048669:C:CTacceptor_gain0.9900
4:77048670:A:Tacceptor_gain0.9900
4:77055376:TGGAA:Tacceptor_gain0.9900
4:77055381:C:CCacceptor_gain0.9900
4:77055948:T:TAdonor_gain0.9900
4:77056013:AT:Adonor_gain0.9900
4:77056014:T:Cdonor_gain0.9900
4:77056321:AGCC:Aacceptor_loss0.9900
4:77056322:GCC:Gacceptor_loss0.9900
4:77056323:CCTAA:Cacceptor_loss0.9900
4:77056324:CTAAA:Cacceptor_loss0.9900
4:77056325:T:Gacceptor_loss0.9900
4:77058500:CACTT:Cdonor_loss0.9900
4:77058501:ACTT:Adonor_loss0.9900
4:77058502:CTTAC:Cdonor_loss0.9900
4:77058503:TTACC:Tdonor_loss0.9900
4:77058504:TAC:Tdonor_loss0.9900
4:77058634:TT:Tacceptor_gain0.9900
4:77058634:TTC:Tacceptor_loss0.9900
4:77058635:TCT:Tacceptor_loss0.9900
4:77058636:C:CCacceptor_gain0.9900

AlphaMissense

2483 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:77056017:A:GL135P1.000
4:77056029:T:AE131V1.000
4:77056031:C:AM130I1.000
4:77056031:C:GM130I1.000
4:77056031:C:TM130I1.000
4:77056267:C:AK100N1.000
4:77056267:C:GK100N1.000
4:77056285:A:CC94W1.000
4:77048634:C:GR240P0.999
4:77055216:A:CS208R0.999
4:77055216:A:TS208R0.999
4:77055218:T:GS208R0.999
4:77056001:C:AW140C0.999
4:77056001:C:GW140C0.999
4:77056003:A:GW140R0.999
4:77056003:A:TW140R0.999
4:77056028:C:AE131D0.999
4:77056028:C:GE131D0.999
4:77056032:A:CM130R0.999
4:77056034:T:AR129S0.999
4:77056034:T:GR129S0.999
4:77056035:C:AR129I0.999
4:77056035:C:GR129T0.999
4:77056274:G:TA98D0.999
4:77056275:C:GA98P0.999
4:77056286:C:TC94Y0.999
4:77056287:A:GC94R0.999
4:77056288:G:CS93R0.999
4:77056288:G:TS93R0.999
4:77056290:T:GS93R0.999

dbSNP variants (sampled 300 via entrez): RS10000115 (4:77069590 T>C,G), RS1000044096 (4:77066034 G>A), RS1000098133 (4:77050681 T>C,G), RS1000136644 (4:77075572 T>A,C,G), RS1000213747 (4:77069080 T>C), RS1000218805 (4:77049526 A>G), RS1000299061 (4:77075478 C>CTCCTCT), RS1000339970 (4:77056992 T>C), RS1000415647 (4:77059936 TCAA>T), RS1000564268 (4:77066007 G>A), RS10005701 (4:77063615 G>A,C,T), RS10006033 (4:77047041 T>C), RS1000904606 (4:77074719 T>A,C), RS1000954554 (4:77067813 A>G), RS1000960844 (4:77072824 G>A)

Disease associations

OMIM: gene MIM:618783 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067138 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

1 potent at pChembl≥5 of 2 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.01Kd9830nMCHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148016: Binding affinity to human CCNI incubated for 45 mins by Kinobead based pull down assaykd9.8301uM

CTD chemical–gene interactions

38 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases methylation, affects cotreatment, decreases expression5
bisphenol Aaffects expression, increases expression, affects cotreatment, decreases expression4
sodium arsenitedecreases expression, increases expression2
cobaltous chloridedecreases expression, increases expression2
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation, increases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideaffects expression, decreases expression2
Cyclosporineincreases expression2
Particulate Matterincreases abundance, increases expression2
GSK-J4increases expression1
bisphenol Faffects cotreatment, decreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
glycidamideincreases expression1
chloropicrinaffects expression1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001increases expression1
dorsomorphindecreases expression, affects cotreatment1
bisphenol Saffects cotreatment, decreases expression1
3-hydroxy-4-prenyl-5-methoxystilbene-2-carboxylic aciddecreases expression1
Sunitinibincreases expression1
Vorinostatdecreases expression1
Acetaminophenincreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Coumestroldecreases expression1
Dexamethasonedecreases expression, affects cotreatment1
Doxorubicindecreases expression1
Dustdecreases expression1
Estradiolaffects expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651058BindingBinding affinity to human CCNI incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B2TNAbcam HEK293T CCNI KOTransformed cell lineFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.