CCNJ

Summary

CCNJ (cyclin J, HGNC:23434) is a protein-coding gene on chromosome 10q24.1, encoding Cyclin-J (Q5T5M9).

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; microtubule organizing center; and nucleus.

Source: NCBI Gene 54619 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 48 total
• MANE Select transcript: NM_001134375

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23434
Approved symbol	CCNJ
Name	cyclin J
Location	10q24.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10895, bA690P14.1
Ensembl gene	ENSG00000107443
Ensembl biotype	protein_coding
OMIM	620395
Entrez	54619

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000265992, ENST00000403870, ENST00000465148, ENST00000868256, ENST00000918738, ENST00000918739, ENST00000918740, ENST00000918741, ENST00000918742, ENST00000918743, ENST00000918744, ENST00000918745

RefSeq mRNA: 3 — MANE Select: NM_001134375 NM_001134375, NM_001134376, NM_019084

CCDS: CCDS44462, CCDS44463, CCDS7445

Canonical transcript exons

ENST00000465148 — 6 exons

Exon	Start	End
ENSE00000811017	96056701	96057000
ENSE00001344659	96050256	96050466
ENSE00001646794	96057088	96057247
ENSE00001876010	96043583	96043719
ENSE00002194219	96044353	96044462
ENSE00003286597	96057830	96060870

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 98.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.0609 / max 125.6237, expressed in 1769 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
106370	9.8666	1768
106371	0.1800	79
106369	0.0143	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	98.76	gold quality
oocyte	CL:0000023	98.20	gold quality
buccal mucosa cell	CL:0002336	89.02	gold quality
embryo	UBERON:0000922	83.66	gold quality
ganglionic eminence	UBERON:0004023	83.40	gold quality
ventricular zone	UBERON:0003053	82.21	gold quality
monocyte	CL:0000576	81.79	gold quality
mononuclear cell	CL:0000842	81.60	gold quality
cortical plate	UBERON:0005343	81.36	gold quality
leukocyte	CL:0000738	81.16	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.94	gold quality
medial globus pallidus	UBERON:0002477	77.24	silver quality
endometrium	UBERON:0001295	77.03	gold quality
globus pallidus	UBERON:0001875	76.06	silver quality
islet of Langerhans	UBERON:0000006	75.89	gold quality
right adrenal gland cortex	UBERON:0035827	75.41	gold quality
stromal cell of endometrium	CL:0002255	75.40	gold quality
granulocyte	CL:0000094	74.81	gold quality
bone marrow	UBERON:0002371	74.78	gold quality
left adrenal gland	UBERON:0001234	74.47	gold quality
adrenal cortex	UBERON:0001235	74.37	gold quality
left adrenal gland cortex	UBERON:0035825	74.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.97	gold quality
right adrenal gland	UBERON:0001233	73.84	gold quality
lymph node	UBERON:0000029	73.81	gold quality
adrenal gland	UBERON:0002369	73.65	gold quality
adrenal tissue	UBERON:0018303	73.39	gold quality
rectum	UBERON:0001052	73.33	gold quality
gall bladder	UBERON:0002110	73.12	gold quality
spleen	UBERON:0002106	73.02	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

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

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784

Literature-anchored findings (GeneRIF, showing 5)

• miR-125b acts as a tumor suppressor in breast tumorigenesis via its novel direct targets ENPEP, CK2-alpha, CCNJ, and MEGF9. (PMID:24098452)
• In conclusion, our results indicated that CCNJ could be a novel prognostic marker of HCC, and this study indicated that triple combination array analysis was effective in detecting new tumor-related genes and their mechanisms. (PMID:25672416)
• CCNJ is a target of miR205 mediated downregulation in bladder cancer cells. (PMID:26469956)
• we identified cyclin J and far upstream element-binding protein 1 (FUBP1) as novel miR-16 targets, which mediate miR-16 antiproliferative effects. (PMID:27157613)
• High Cyclin J expression is associated with drug resistance in non-small cell lung cancer. (PMID:28202053)

Cross-species orthologs

15 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccnj	ENSDARG00000059917
mus_musculus	Ccnj	ENSMUSG00000025010
rattus_norvegicus	Ccnj	ENSRNOG00000076838
drosophila_melanogaster	CycA	FBGN0000404
drosophila_melanogaster	CycB	FBGN0000405
drosophila_melanogaster	CycD	FBGN0010315
drosophila_melanogaster	CycE	FBGN0010382
caenorhabditis_elegans		WBGENE00000863
caenorhabditis_elegans		WBGENE00000864
caenorhabditis_elegans		WBGENE00000865
caenorhabditis_elegans		WBGENE00000866
caenorhabditis_elegans	cyb-2.2	WBGENE00000867
caenorhabditis_elegans		WBGENE00000870
caenorhabditis_elegans	cye-1	WBGENE00000871
caenorhabditis_elegans		WBGENE00017259

Paralogs (18): CCNE1 (ENSG00000105173), CCNP (ENSG00000105219), CCND1 (ENSG00000110092), CCND3 (ENSG00000112576), CCNG1 (ENSG00000113328), CCNI (ENSG00000118816), 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-J — Q5T5M9 (reviewed: Q5T5M9)

All UniProt accessions (1): Q5T5M9

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the cyclin family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5T5M9-1	1	yes
Q5T5M9-2	2
Q5T5M9-3	3

RefSeq proteins (3): NP_001127847, NP_001127848, NP_061957 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004367	Cyclin_C-dom	Domain
IPR006671	Cyclin_N	Domain
IPR013763	Cyclin-like_dom	Domain
IPR036915	Cyclin-like_sf	Homologous_superfamily
IPR039361	Cyclin	Family

Pfam: PF00134, PF02984

UniProt features (4 total): splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T5M9-F1	73.34	0.59

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 220 (showing top): ACTACCT_MIR196A_MIR196B, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_CELL_CYCLE_PHASE_TRANSITION, AAAYRNCTG_UNKNOWN, CAGCTG_AP4_Q5, GOCC_MICROTUBULE_ORGANIZING_CENTER, CAGCAGG_MIR370, SOX9_B1, MCAATNNNNNGCG_UNKNOWN, GOBP_CELL_CYCLE_G1_S_PHASE_TRANSITION, GOBP_MITOTIC_CELL_CYCLE, RASHI_RESPONSE_TO_IONIZING_RADIATION_6, SOX5_01, GOCC_TRANSFERASE_COMPLEX_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, GOCC_TRANSFERASE_COMPLEX

GO Biological Process (1): G1/S transition of mitotic cell cycle (GO:0000082)

GO Molecular Function (1): cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)

GO Cellular Component (4): cyclin-dependent protein kinase holoenzyme complex (GO:0000307), nucleus (GO:0005634), cytoplasm (GO:0005737), microtubule organizing center (GO:0005815)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
mitotic cell cycle	1
mitotic cell cycle phase transition	1
cell cycle G1/S phase transition	1
cyclin-dependent protein serine/threonine kinase activity	1
cyclin-dependent protein kinase regulator activity	1
serine/threonine protein kinase complex	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
microtubule cytoskeleton	1

Protein interactions and networks

STRING

864 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCNJ	MEGF9	Q9H1U4	571
CCNJ	FUBP1	Q96AE4	418
CCNJ	CSNK2A2	P19784	384
CCNJ	ZNF408	Q9H9D4	374
CCNJ	GRAMD4	Q6IC98	374
CCNJ	ENPEP	Q07075	371
CCNJ	CC2D2B	Q6DHV5	351
CCNJ	CCNC	P24863	340
CCNJ	ACOT13	Q9NPJ3	321
CCNJ	CCNH	P51946	317
CCNJ	AKAP7	O43687	309
CCNJ	BTBD9	Q96Q07	306
CCNJ	GP9	P14770	301
CCNJ	NMUR1	Q9HB89	301
CCNJ	NHSL3	Q9P206	294

IntAct

11 interactions, top by confidence:

A	B	Type	Score
CDK2	CCNE2	psi-mi:“MI:0914”(association)	0.940
CDK2	GMNN	psi-mi:“MI:0914”(association)	0.640
GORASP1	PPP6R2	psi-mi:“MI:0914”(association)	0.530
CCNJ	POTEF	psi-mi:“MI:0915”(physical association)	0.400
GORASP1	RTCA	psi-mi:“MI:0914”(association)	0.350
BCL11B	MTA2	psi-mi:“MI:0914”(association)	0.350
NOBOX	CDK2	psi-mi:“MI:0914”(association)	0.350
GORASP1	PRORP	psi-mi:“MI:0914”(association)	0.350
CCNJ	ATE1	psi-mi:“MI:0914”(association)	0.350
SLC30A5	NBAS	psi-mi:“MI:0914”(association)	0.350

BioGRID (12): CCNJ (Affinity Capture-MS), POTEF (Affinity Capture-MS), SPECC1L (Affinity Capture-MS), CCNJ (Affinity Capture-MS), CCNJ (Affinity Capture-MS), POTEF (Affinity Capture-MS), CCNJ (Affinity Capture-MS), CCNJ (Affinity Capture-MS), CCNJ (Affinity Capture-MS), CCNJ (Affinity Capture-RNA), CCNJ (Affinity Capture-RNA), CCNJ (Affinity Capture-MS)

ESM2 similar proteins: A5PK16, O08918, O42575, O96020, P24385, P24864, P25322, P30279, P30280, P30282, P39948, P39949, P39950, P41002, P47794, P48961, P49706, P49707, P50755, P50756, P51944, P51945, P51959, P53782, P55169, Q04827, Q0P5D3, Q16589, Q2KI22, Q32NJ2, Q32NM1, Q52QT8, Q5E9I1, Q5E9K7, Q5R5D0, Q5R6J5, Q5SRT8, Q5T5M9, Q5XGG5, Q61457

Diamond homologs: C4YR54, O48790, P0CY18, P13351, P13365, P20437, P20438, P24861, P24865, P24868, P24869, P24870, P24871, P25009, P25011, P25012, P30284, P32943, P34800, P34801, P37881, P39963, P43062, P51986, Q06374, Q0DH40, Q0JIF2, Q10Q62, Q10QA2, Q39068, Q39069, Q39070, Q3TZI6, Q59YH3, Q5A0A9, Q5A1N6, Q5T5M9, Q659K0, Q6DFJ9, Q810T2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	37
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

918 predictions. Top by Δscore:

Variant	Effect	Δscore
10:96044458:ACAAG:A	donor_loss	1.0000
10:96044459:CAAG:C	donor_loss	1.0000
10:96044460:AAGGT:A	donor_loss	1.0000
10:96044461:AGGT:A	donor_loss	1.0000
10:96044462:GGTAA:G	donor_loss	1.0000
10:96044463:GT:G	donor_loss	1.0000
10:96044464:T:A	donor_loss	1.0000
10:96050463:GCAA:G	donor_gain	1.0000
10:96050464:CAAG:C	donor_loss	1.0000
10:96050465:AAGT:A	donor_loss	1.0000
10:96050466:AGTA:A	donor_loss	1.0000
10:96050467:G:GG	donor_gain	1.0000
10:96050467:G:T	donor_loss	1.0000
10:96050468:T:A	donor_loss	1.0000
10:96056985:G:GT	donor_gain	1.0000
10:96056997:CAAG:C	donor_loss	1.0000
10:96057001:GTGG:G	donor_loss	1.0000
10:96057245:GAT:G	donor_gain	1.0000
10:96057248:G:GG	donor_gain	1.0000
10:96057821:A:AG	acceptor_gain	1.0000
10:96057821:AC:A	acceptor_gain	1.0000
10:96057822:C:CA	acceptor_gain	1.0000
10:96057822:C:G	acceptor_gain	1.0000
10:96057825:TTCAG:T	acceptor_loss	1.0000
10:96057826:TCA:T	acceptor_loss	1.0000
10:96057827:CAGC:C	acceptor_loss	1.0000
10:96057828:A:AG	acceptor_gain	1.0000
10:96057828:AG:A	acceptor_loss	1.0000
10:96057828:AGC:A	acceptor_gain	1.0000
10:96057829:G:GA	acceptor_gain	1.0000

AlphaMissense

2488 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:96044452:T:C	L20P	1.000
10:96050305:G:C	R40T	1.000
10:96050305:G:T	R40I	1.000
10:96050306:A:C	R40S	1.000
10:96050306:A:T	R40S	1.000
10:96050328:G:C	A48P	1.000
10:96050374:T:C	L63P	1.000
10:96050376:G:C	A64P	1.000
10:96050389:T:C	L68P	1.000
10:96050392:A:C	D69A	1.000
10:96050392:A:T	D69V	1.000
10:96050431:T:C	L82P	1.000
10:96050451:T:C	C89R	1.000
10:96050452:G:A	C89Y	1.000
10:96050453:C:G	C89W	1.000
10:96050455:T:C	L90P	1.000
10:96056705:A:C	K95N	1.000
10:96056705:A:T	K95N	1.000
10:96056730:C:T	P104S	1.000
10:96056731:C:A	P104H	1.000
10:96056746:T:C	L109P	1.000
10:96056838:T:A	W140R	1.000
10:96056838:T:C	W140R	1.000
10:96056840:G:C	W140C	1.000
10:96056840:G:T	W140C	1.000
10:96056854:C:A	P145Q	1.000
10:96057145:C:G	S202W	1.000
10:96057148:G:C	R203T	1.000
10:96057148:G:T	R203M	1.000
10:96057149:G:C	R203S	1.000

dbSNP variants (sampled 300 via entrez): RS1000079410 (10:96042949 G>A,C), RS1000187916 (10:96051560 T>C), RS1000237337 (10:96060271 C>T), RS1000296120 (10:96042755 C>G,T), RS1000391610 (10:96042390 A>G), RS1000510206 (10:96047422 T>C), RS1000540863 (10:96047186 A>G), RS1000552190 (10:96055664 T>A), RS1000611042 (10:96055356 C>A,T), RS1000772419 (10:96060572 G>A), RS1000809700 (10:96054035 C>G), RS1001055142 (10:96041601 A>G), RS1001073455 (10:96054442 G>A,C), RS1001185405 (10:96044889 A>C,T), RS1001453952 (10:96047869 A>G)

Disease associations

OMIM: gene MIM:620395 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST005863_28	Menopause (age at onset)	3.000000e-22
GCST005863_32	Menopause (age at onset)	2.000000e-20

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004704	age at menopause

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
Benzo(a)pyrene	decreases expression, decreases methylation	2
Particulate Matter	decreases reaction, increases expression, increases abundance	2
trichostatin A	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
entinostat	decreases expression	1
scriptaid	affects expression	1
motexafin gadolinium	affects cotreatment, decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
bisphenol S	affects cotreatment, increases expression	1
jinfukang	decreases expression	1
Leflunomide	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Aspirin	increases expression	1
Vehicle Emissions	decreases reaction, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Estradiol	increases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	increases expression, affects cotreatment	1
Lead	affects expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Melphalan	increases expression	1
Methyl Methanesulfonate	decreases expression	1
Smoke	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_SH44	HAP1 CCNJ (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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