SPDYE6

Summary

SPDYE6 (speedy/RINGO cell cycle regulator family member E6, HGNC:35465) is a protein-coding gene on chromosome 7q22.1, encoding Speedy protein E6 (P0CI01).

This gene encodes a cell cycle regulatory protein which plays an important role in cell cycle progression by binding and activating cyclin-dependent kinases. The encoded protein belongs to a family of cyclin-dependent kinase regulators that contain a speedy box domain which is required for cyclin-dependent kinase activation.

Source: NCBI Gene 729597 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_001146210

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:35465
Approved symbol	SPDYE6
Name	speedy/RINGO cell cycle regulator family member E6
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000260097
Ensembl biotype	protein_coding
Entrez	729597

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000563237

RefSeq mRNA: 1 — MANE Select: NM_001146210 NM_001146210

CCDS: CCDS78265

Canonical transcript exons

ENST00000563237 — 8 exons

Exon	Start	End
ENSE00003502918	102348284	102348677
ENSE00003516710	102352066	102352124
ENSE00003566676	102353158	102353388
ENSE00003639085	102350728	102350813
ENSE00003648665	102354703	102354921
ENSE00003755017	102348057	102348161
ENSE00003756502	102345746	102347221
ENSE00003758297	102355864	102356444

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 76.84.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bone marrow cell	CL:0002092	76.84	gold quality
skeletal muscle tissue	UBERON:0001134	75.66	gold quality
tonsil	UBERON:0002372	72.29	gold quality
colonic epithelium	UBERON:0000397	71.07	gold quality
muscle tissue	UBERON:0002385	70.47	gold quality
bone marrow	UBERON:0002371	69.75	gold quality
granulocyte	CL:0000094	69.18	gold quality
stromal cell of endometrium	CL:0002255	68.85	gold quality
hindlimb stylopod muscle	UBERON:0004252	68.23	gold quality
testis	UBERON:0000473	67.66	gold quality
left testis	UBERON:0004533	67.65	gold quality
monocyte	CL:0000576	67.21	gold quality
leukocyte	CL:0000738	67.17	gold quality
blood	UBERON:0000178	66.83	gold quality
adrenal tissue	UBERON:0018303	66.80	gold quality
right testis	UBERON:0004534	66.79	gold quality
lower esophagus mucosa	UBERON:0035834	66.12	gold quality
gastrocnemius	UBERON:0001388	65.66	gold quality
muscle of leg	UBERON:0001383	65.50	gold quality
mucosa of transverse colon	UBERON:0004991	65.28	gold quality
spleen	UBERON:0002106	65.16	gold quality
right lobe of thyroid gland	UBERON:0001119	64.55	gold quality
metanephros cortex	UBERON:0010533	63.38	gold quality
cortex of kidney	UBERON:0001225	63.28	gold quality
body of pancreas	UBERON:0001150	62.77	gold quality
liver	UBERON:0002107	62.22	gold quality
vermiform appendix	UBERON:0001154	62.07	gold quality
small intestine	UBERON:0002108	61.94	gold quality
thyroid gland	UBERON:0002046	61.86	gold quality
small intestine Peyer’s patch	UBERON:0003454	61.86	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.41

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

103 targeting SPDYE6, 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-3924	100.00	72.09	2394
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spdye4b	ENSMUSG00000029586
mus_musculus	Spdye4a	ENSMUSG00000039296
rattus_norvegicus	Spdye4	ENSRNOG00000058563

Paralogs (18): SPDYE1 (ENSG00000136206), SPDYE5 (ENSG00000170092), SPDYE2B (ENSG00000173678), SPDYE4 (ENSG00000183318), SPDYE12 (ENSG00000184616), SPDYE16 (ENSG00000185040), SPDYE17 (ENSG00000186645), SPDYE2 (ENSG00000205238), SPDYE18 (ENSG00000205482), SPDYE3 (ENSG00000214300), SPDYE21 (ENSG00000230358), SPDYE9 (ENSG00000262461), SPDYE8 (ENSG00000273520), SPDYE10 (ENSG00000274570), SPDYE11 (ENSG00000275976), SPDYE15 (ENSG00000286014), SPDYE13 (ENSG00000286038), SPDYE14 (ENSG00000286137)

Protein

Protein identifiers

Speedy protein E6 — P0CI01 (reviewed: P0CI01)

All UniProt accessions (1): P0CI01

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the Speedy/Ringo family.

RefSeq proteins (1): NP_001139682* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR020984	Speedy	Family
IPR057742	Speedy_E	Family

Pfam: PF11357

UniProt features (4 total): compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CI01-F1	61.43	0.22

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): GOMF_KINASE_BINDING, MIR153_5P, MIR3662, MIR1277_5P, MIR3121_3P, MIR4753_3P, MIR5692B_MIR5692C, MIR3924, MIR410_3P, MIR577, MIR488_3P, MIR5197_3P, MIR548BA, MIR548AI_MIR570_5P, MIR548AG

GO Biological Process (1): positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)

GO Molecular Function (2): protein kinase binding (GO:0019901), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of cyclin-dependent protein serine/threonine kinase activity	1
cyclin-dependent protein serine/threonine kinase activity	1
positive regulation of cell cycle	1
positive regulation of protein serine/threonine kinase activity	1
positive regulation of cyclin-dependent protein kinase activity	1
kinase binding	1
binding	1

Protein interactions and networks

STRING

52 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPDYE6	G2E3	Q7L622	507
SPDYE6	VWA5A	O00534	507
SPDYE6	VPS37A	Q8NEZ2	477
SPDYE6	ZNF19	P17023	434
SPDYE6	ATF7IP	Q6VMQ6	395
SPDYE6	PEA15	Q15121	370
SPDYE6	WDFY1	Q8IWB7	271
SPDYE6	SLC43A3	Q8NBI5	261
SPDYE6	ELMO2	Q96JJ3	224
SPDYE6	AKAP7	O43687	224
SPDYE6	HMGN1	P05114	179
SPDYE6	NDUFA13	Q9P0J0	175
SPDYE6	KLRK1	P26718	166
SPDYE6	NUTM2G	Q5VZR2	102
SPDYE6	MAPRE3	Q9UPY8	0
SPDYE6	SPDYE1	Q8NFV5	0

IntAct

13 interactions, top by confidence:

A	B	Type	Score
SPDYE6	MAPRE3	psi-mi:“MI:0915”(physical association)	0.560
SPDYE6	MAPRE1	psi-mi:“MI:0915”(physical association)	0.560
SPDYE6	APPBP2	psi-mi:“MI:0915”(physical association)	0.560
SPDYE6	KRTAP17-1	psi-mi:“MI:0915”(physical association)	0.560
SPDYE6	MAPRE3	psi-mi:“MI:0915”(physical association)	0.000
SPDYE6	MAPRE1	psi-mi:“MI:0915”(physical association)	0.000
SPDYE6	APPBP2	psi-mi:“MI:0915”(physical association)	0.000
SPDYE6	KRTAP17-1	psi-mi:“MI:0915”(physical association)	0.000

ESM2 similar proteins: A0A0J9YY54, A0A494C086, A0A494C0Z2, A0A494C191, A6NHP3, A6NIY4, A6NJR5, A6NNV3, B4DH59, F6SZT2, P0C6Y7, P0CI01, P0DKJ7, P0DKJ8, P0DTA3, P0DUD1, P0DUD2, P0DUD3, P0DUD4, P0DUX0, P0DUX1, P0DV79, P79386, Q08AG5, Q13342, Q16666, Q3BBV2, Q495Y8, Q587J8, Q5JRC9, Q5QGU6, Q5RD14, Q5RKG3, Q63HK3, Q6ITT4, Q7TQI8, Q86T75, Q8IWY8, Q8N660, Q8NFV5

Diamond homologs: A0A494C086, A0A494C0Z2, A0A494C191, A6NHP3, A6NIY4, A6NJR5, A6NKU9, A6NLX3, A6NNV3, P0CI01, P0DTA3, P0DUD1, P0DUD2, P0DUD3, P0DUD4, P0DUX0, P0DUX1, P0DV79, Q495Y7, Q495Y8, Q5IBH6, Q5IBH7, Q5MJ68, Q5MJ70, Q8NFV5, Q8R496, Q9PU13, Q9YGL1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

884 predictions. Top by Δscore:

Variant	Effect	Δscore
7:102348678:C:CC	acceptor_gain	1.0000
7:102348279:CTCA:C	donor_loss	0.9900
7:102348280:TCA:T	donor_loss	0.9900
7:102348281:CA:C	donor_loss	0.9900
7:102348282:A:T	donor_loss	0.9900
7:102348282:ACCT:A	donor_gain	0.9900
7:102348283:C:A	donor_loss	0.9900
7:102348283:CCTC:C	donor_gain	0.9900
7:102348607:T:TA	donor_gain	0.9900
7:102348673:GGTAG:G	acceptor_gain	0.9900
7:102348674:GTAGC:G	acceptor_loss	0.9900
7:102348675:TAG:T	acceptor_gain	0.9900
7:102348675:TAGCT:T	acceptor_loss	0.9900
7:102348676:AGC:A	acceptor_loss	0.9900
7:102348677:GCTG:G	acceptor_loss	0.9900
7:102348678:CTGAG:C	acceptor_loss	0.9900
7:102348679:T:A	acceptor_loss	0.9900
7:102352125:C:CC	acceptor_gain	0.9900
7:102355860:TCA:T	donor_loss	0.9900
7:102355861:CACC:C	donor_loss	0.9900
7:102355896:T:TA	donor_gain	0.9900
7:102348674:GTAG:G	acceptor_gain	0.9800
7:102352121:TCCT:T	acceptor_gain	0.9800
7:102352122:CCT:C	acceptor_gain	0.9800
7:102352122:CCTC:C	acceptor_gain	0.9800
7:102352123:CTC:C	acceptor_gain	0.9800
7:102352124:TCT:T	acceptor_gain	0.9800
7:102353160:AGCAG:A	donor_gain	0.9800
7:102354702:CCAAG:C	donor_gain	0.9800
7:102355891:C:CT	donor_gain	0.9800

AlphaMissense

2664 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:102352102:G:C	F211L	0.989
7:102352102:G:T	F211L	0.989
7:102352104:A:G	F211L	0.989
7:102353171:G:C	F199L	0.982
7:102353171:G:T	F199L	0.982
7:102353173:A:G	F199L	0.982
7:102350784:G:C	F233L	0.981
7:102350784:G:T	F233L	0.981
7:102350786:A:G	F233L	0.981
7:102352103:A:G	F211S	0.979
7:102348635:T:A	K266N	0.975
7:102348635:T:G	K266N	0.975
7:102350736:G:C	F249L	0.968
7:102350736:G:T	F249L	0.968
7:102350738:A:G	F249L	0.968
7:102348617:G:C	F272L	0.964
7:102348617:G:T	F272L	0.964
7:102348619:A:G	F272L	0.964
7:102352091:T:A	D215V	0.956
7:102352091:T:G	D215A	0.956
7:102352100:A:G	L212S	0.952
7:102348636:T:A	K266I	0.943
7:102350739:G:C	F248L	0.943
7:102350739:G:T	F248L	0.943
7:102350741:A:G	F248L	0.943
7:102350789:A:C	Y232D	0.943
7:102350785:A:G	F233S	0.942
7:102353172:A:G	F199S	0.942
7:102352121:T:C	D205G	0.938
7:102350779:C:G	R235P	0.937

dbSNP variants (sampled 300 via entrez): RS10232123 (7:102350313 A>G), RS10232255 (7:102350440 A>G), RS10232260 (7:102350452 A>G), RS10261877 (7:102350363 G>A,C), RS1059797 (7:102347229 C>G,T), RS1062116 (7:102356478 C>G), RS111359096 (7:102357982 T>G), RS111385834 (7:102346895 C>G,T), RS111415850 (7:102347298 A>C,G), RS111422632 (7:102351587 T>A,C,G), RS111484825 (7:102352418 T>A), RS111817273 (7:102348943 A>G), RS111922879 (7:102349579 C>G), RS112077306 (7:102356097 A>G), RS112263267 (7:102351517 G>A)

Disease associations

OMIM: gene `` | 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: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
ICG 001	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1

Clinical trials (associated diseases)

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