SPDYE2B

Summary

SPDYE2B (speedy/RINGO cell cycle regulator family member E2B, HGNC:48334) is a protein-coding gene on chromosome 7q22.1, encoding Speedy protein E2B (A6NHP3).

Predicted to enable protein kinase binding activity.

Source: NCBI Gene 100310812 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001166339

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:48334
Approved symbol	SPDYE2B
Name	speedy/RINGO cell cycle regulator family member E2B
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000173678
Ensembl biotype	protein_coding
Entrez	100310812

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000436228, ENST00000455020, ENST00000507450

RefSeq mRNA: 1 — MANE Select: NM_001166339 NM_001166339

CCDS: CCDS59507

Canonical transcript exons

ENST00000507450 — 9 exons

Exon	Start	End
ENSE00002443019	102656248	102656306
ENSE00002449921	102651928	102652508
ENSE00002455729	102653451	102653669
ENSE00002464376	102650319	102650377
ENSE00002486994	102657551	102657636
ENSE00002488441	102659690	102660083
ENSE00002501224	102654984	102655214
ENSE00002507141	102660206	102660310
ENSE00002518950	102661146	102662625

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 77.96.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.96	gold quality
bone marrow cell	CL:0002092	75.27	gold quality
skeletal muscle tissue	UBERON:0001134	70.34	gold quality
colonic epithelium	UBERON:0000397	68.24	gold quality
bone marrow	UBERON:0002371	67.15	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	66.36	silver quality
sural nerve	UBERON:0015488	65.61	gold quality
blood	UBERON:0000178	65.25	gold quality
muscle tissue	UBERON:0002385	64.92	gold quality
stromal cell of endometrium	CL:0002255	63.04	gold quality
granulocyte	CL:0000094	60.15	gold quality
hindlimb stylopod muscle	UBERON:0004252	60.11	gold quality
muscle of leg	UBERON:0001383	59.83	gold quality
tonsil	UBERON:0002372	59.63	gold quality
gastrocnemius	UBERON:0001388	59.38	gold quality
lower esophagus mucosa	UBERON:0035834	57.11	gold quality
leukocyte	CL:0000738	56.92	gold quality
vermiform appendix	UBERON:0001154	56.62	gold quality
monocyte	CL:0000576	56.60	gold quality
right uterine tube	UBERON:0001302	55.76	gold quality
right lobe of thyroid gland	UBERON:0001119	55.32	gold quality
liver	UBERON:0002107	54.92	gold quality
ventricular zone	UBERON:0003053	54.34	gold quality
urinary bladder	UBERON:0001255	54.06	gold quality
stomach	UBERON:0000945	54.05	gold quality
heart left ventricle	UBERON:0002084	54.00	gold quality
cortex of kidney	UBERON:0001225	53.50	gold quality
small intestine	UBERON:0002108	53.47	gold quality
mucosa of stomach	UBERON:0001199	53.20	gold quality
apex of heart	UBERON:0002098	53.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.17

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting SPDYE2B, 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-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-6505-5P	99.73	69.25	1595
HSA-MIR-363-5P	99.46	64.51	1015
HSA-MIR-4769-3P	97.95	68.17	1002
HSA-MIR-6817-5P	97.95	67.86	1026
HSA-MIR-6747-3P	97.73	64.84	1596
HSA-MIR-22-5P	97.67	68.92	1355
HSA-MIR-7154-3P	97.65	65.02	985
HSA-MIR-346	97.01	66.97	662
HSA-MIR-6736-3P	96.98	65.22	1342

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), SPDYE4 (ENSG00000183318), SPDYE12 (ENSG00000184616), SPDYE16 (ENSG00000185040), SPDYE17 (ENSG00000186645), SPDYE2 (ENSG00000205238), SPDYE18 (ENSG00000205482), SPDYE3 (ENSG00000214300), SPDYE21 (ENSG00000230358), SPDYE6 (ENSG00000260097), SPDYE9 (ENSG00000262461), SPDYE8 (ENSG00000273520), SPDYE10 (ENSG00000274570), SPDYE11 (ENSG00000275976), SPDYE15 (ENSG00000286014), SPDYE13 (ENSG00000286038), SPDYE14 (ENSG00000286137)

Protein

Protein identifiers

Speedy protein E2B — A6NHP3 (reviewed: A6NHP3)

All UniProt accessions (1): A6NHP3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the Speedy/Ringo family.

Isoforms (2)

UniProt ID	Names	Canonical?
A6NHP3-1	1	yes
A6NHP3-2	2

RefSeq proteins (1): NP_001159811* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR020984	Speedy	Family
IPR057742	Speedy_E	Family

Pfam: PF11357

UniProt features (5 total): compositionally biased region 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NHP3-F1	61.12	0.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): GOMF_KINASE_BINDING, LU_EZH2_TARGETS_DN, MIR6736_3P, MIR346, chr7q22

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

GO Molecular Function (1): protein kinase binding (GO:0019901)

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

Protein interactions and networks

STRING

20 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPDYE2B	NUTM2G	Q5VZR2	102
SPDYE2B	SPDYE1	Q8NFV5	0
SPDYE2B	CDK2	P24941	0
SPDYE2B	CDC25C	P30307	0
SPDYE2B	SPDYA	Q5MJ70	0
SPDYE2B	SPDYC	Q5MJ68	0
SPDYE2B	CDK1	P06493	0
SPDYE2B	SPDYE2	Q495Y8	0
SPDYE2B	SPDYE5	A6NIY4	0
SPDYE2B	SPDYE6	P0CI01	0

IntAct

2 interactions, top by confidence:

A	B	Type	Score
SPDYE2B	PCNA	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (5): SPDYE2B (Two-hybrid), SPDYE2B (Two-hybrid), SPDYE2B (Two-hybrid), KRTAP17-1 (Two-hybrid), SPDYE2B (Negative Genetic)

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1444 predictions. Top by Δscore:

Variant	Effect	Δscore
7:102656246:A:AG	acceptor_gain	0.9900
7:102656247:G:GG	acceptor_gain	0.9900
7:102659688:A:AG	acceptor_gain	0.9900
7:102659689:G:GA	acceptor_gain	0.9900
7:102659689:GCT:G	acceptor_gain	0.9900
7:102659759:G:GT	donor_gain	0.9900
7:102660080:GGAG:G	donor_gain	0.9900
7:102660081:GAGG:G	donor_gain	0.9900
7:102660083:GGTG:G	donor_loss	0.9900
7:102660084:G:GA	donor_loss	0.9900
7:102660085:T:A	donor_loss	0.9900
7:102651982:GCTT:G	donor_gain	0.9800
7:102652475:G:GT	donor_gain	0.9800
7:102652480:G:GA	donor_gain	0.9800
7:102655207:GCTGC:G	donor_gain	0.9800
7:102656246:AGAG:A	acceptor_gain	0.9800
7:102656247:GAGG:G	acceptor_gain	0.9800
7:102657637:G:GG	donor_gain	0.9800
7:102659684:CCTCA:C	acceptor_loss	0.9800
7:102659685:CTCA:C	acceptor_loss	0.9800
7:102659686:TCAGC:T	acceptor_loss	0.9800
7:102659687:CA:C	acceptor_loss	0.9800
7:102659689:GCTAC:G	acceptor_gain	0.9800
7:102652479:T:TA	donor_gain	0.9700
7:102652506:CAG:C	donor_loss	0.9700
7:102652507:AGG:A	donor_loss	0.9700
7:102652508:GGTGA:G	donor_loss	0.9700
7:102652509:G:GA	donor_loss	0.9700
7:102653665:GCTTG:G	donor_gain	0.9700
7:102655163:C:T	donor_gain	0.9700

AlphaMissense

2662 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:102656268:T:C	F211L	0.989
7:102656270:C:A	F211L	0.989
7:102656270:C:G	F211L	0.989
7:102655199:T:C	F199L	0.987
7:102655201:C:A	F199L	0.987
7:102655201:C:G	F199L	0.987
7:102656269:T:C	F211S	0.980
7:102657578:T:C	F233L	0.979
7:102657580:C:A	F233L	0.979
7:102657580:C:G	F233L	0.979
7:102659732:A:C	K266N	0.975
7:102659732:A:T	K266N	0.975
7:102656281:A:T	D215V	0.971
7:102656281:A:C	D215A	0.970
7:102657626:T:C	F249L	0.967
7:102657628:C:A	F249L	0.967
7:102657628:C:G	F249L	0.967
7:102655200:T:C	F199S	0.962
7:102656302:A:T	D222V	0.962
7:102656272:T:C	L212S	0.961
7:102660238:G:C	W394C	0.956
7:102660238:G:T	W394C	0.956
7:102656280:G:C	D215H	0.955
7:102659748:T:C	F272L	0.954
7:102659750:C:A	F272L	0.954
7:102659750:C:G	F272L	0.954
7:102657579:T:C	F233S	0.945
7:102656282:C:A	D215E	0.944
7:102656282:C:G	D215E	0.944
7:102655209:T:C	L202P	0.943

dbSNP variants (sampled 300 via entrez): RS1044151489 (7:102656362 C>T), RS1059798 (7:102661090 T>C), RS111553311 (7:102660858 A>G), RS111656884 (7:102657102 G>A), RS111666395 (7:102662788 T>C), RS111737170 (7:102654961 C>G,T), RS111757010 (7:102661671 G>T), RS112021919 (7:102652675 C>T), RS112094731 (7:102654733 A>C,G), RS112209185 (7:102662477 C>T), RS112380295 (7:102651696 T>C), RS112436737 (7:102648963 C>T), RS112471566 (7:102651577 C>T), RS112521196 (7:102652251 C>T), RS112548817 (7:102648666 T>G)

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
cordycepin	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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