SPDYE16

Summary

SPDYE16 (speedy/RINGO cell cycle regulator family member E16, HGNC:51512) is a protein-coding gene on chromosome 7q11.23, encoding Speedy protein E16 (A6NNV3).

Predicted to enable protein kinase binding activity.

Source: NCBI Gene 102723555 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001394943

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:51512
Approved symbol	SPDYE16
Name	speedy/RINGO cell cycle regulator family member E16
Location	7q11.23
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000185040
Ensembl biotype	protein_coding
Entrez	102723555

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000515340, ENST00000632547, ENST00000633306

RefSeq mRNA: 2 — MANE Select: NM_001394943 NM_001351597, NM_001394943

CCDS: CCDS94129

Canonical transcript exons

ENST00000633306 — 9 exons

Exon	Start	End
ENSE00002031483	76538586	76538816
ENSE00002032353	76537493	76537551
ENSE00002504774	76536172	76536257
ENSE00003779097	76540128	76540346
ENSE00003780186	76533876	76534119
ENSE00003780906	76533649	76533753
ENSE00003781036	76531313	76532794
ENSE00003926299	76541300	76541880
ENSE00003937274	76543176	76543297

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 80.82.

Top tissues by expression

134 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	80.82	gold quality
sural nerve	UBERON:0015488	76.68	gold quality
skeletal muscle tissue	UBERON:0001134	74.68	gold quality
bone marrow cell	CL:0002092	73.12	gold quality
hindlimb stylopod muscle	UBERON:0004252	72.77	gold quality
muscle tissue	UBERON:0002385	71.48	gold quality
blood	UBERON:0000178	71.06	gold quality
stromal cell of endometrium	CL:0002255	71.01	gold quality
gastrocnemius	UBERON:0001388	70.86	gold quality
tonsil	UBERON:0002372	70.78	gold quality
muscle of leg	UBERON:0001383	70.76	gold quality
granulocyte	CL:0000094	70.05	gold quality
adrenal tissue	UBERON:0018303	69.92	gold quality
right lobe of thyroid gland	UBERON:0001119	69.12	gold quality
lower esophagus mucosa	UBERON:0035834	69.02	gold quality
bone marrow	UBERON:0002371	68.98	gold quality
leukocyte	CL:0000738	68.38	gold quality
monocyte	CL:0000576	68.34	gold quality
left lobe of thyroid gland	UBERON:0001120	67.77	gold quality
thyroid gland	UBERON:0002046	67.61	gold quality
cortex of kidney	UBERON:0001225	67.32	gold quality
mucosa of transverse colon	UBERON:0004991	67.26	gold quality
spleen	UBERON:0002106	66.90	gold quality
colonic epithelium	UBERON:0000397	66.71	silver quality
right ovary	UBERON:0002118	66.69	gold quality
liver	UBERON:0002107	66.38	gold quality
body of pancreas	UBERON:0001150	66.36	gold quality
esophagus mucosa	UBERON:0002469	66.21	gold quality
small intestine Peyer’s patch	UBERON:0003454	66.17	gold quality
small intestine	UBERON:0002108	66.04	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-CURD-11	no	8.89
E-ANND-3	no	2.85

Regulation

Is transcription factor: no

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), 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 E16 — A6NNV3 (reviewed: A6NNV3)

Alternative names: Speedy/RINGO cell cycle regulator family member E16

All UniProt accessions (3): A6NNV3, A0A0J9YWM7, A0A0J9YYF2

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the Speedy/Ringo family.

RefSeq proteins (2): NP_001338526, NP_001381872* (*=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-A6NNV3-F1	60.51	0.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): chr7q11, GOMF_KINASE_BINDING

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

86 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPDYE16	N4BP2	Q86UW6	447
SPDYE16	PLPPR4	Q7Z2D5	397
SPDYE16	CENPN	Q96H22	321
SPDYE16	NUTM2F	A1L443	318
SPDYE16	NUTM2G	Q5VZR2	318
SPDYE16	CDADC1	Q9BWV3	316
SPDYE16	CATSPERT	Q53TS8	311
SPDYE16	SAXO2	Q658L1	305
SPDYE16	ZWINT	O95229	305
SPDYE16	GPANK1	O95872	288
SPDYE16	KLHDC1	Q8N7A1	285
SPDYE16	HJURP	Q8NCD3	279
SPDYE16	ACTG2	P12718	272
SPDYE16	GALNT8	Q9NY28	266
SPDYE16	STC2	O76061	257

IntAct

0 interactions, top by confidence:

BioGRID (2): LOC102723555 (Affinity Capture-MS), LOC102723555 (Affinity Capture-RNA)

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

690 predictions. Top by Δscore:

Variant	Effect	Δscore
7:76534115:GGTAG:G	acceptor_gain	1.0000
7:76534117:TAG:T	acceptor_gain	1.0000
7:76534119:GC:G	acceptor_loss	1.0000
7:76534120:C:CC	acceptor_gain	1.0000
7:76534120:CTGA:C	acceptor_loss	1.0000
7:76540127:CCAAG:C	donor_gain	1.0000
7:76540131:G:C	donor_gain	1.0000
7:76534116:GTAG:G	acceptor_gain	0.9900
7:76534118:AG:A	acceptor_gain	0.9900
7:76536170:A:AC	donor_gain	0.9900
7:76536171:C:CC	donor_gain	0.9900
7:76537552:C:CC	acceptor_gain	0.9900
7:76540145:T:TA	donor_gain	0.9900
7:76533874:ACCT:A	donor_gain	0.9800
7:76533875:CCTC:C	donor_gain	0.9800
7:76533974:T:TA	donor_gain	0.9800
7:76534050:C:A	donor_gain	0.9800
7:76537548:TCCT:T	acceptor_gain	0.9800
7:76537549:CCTC:C	acceptor_gain	0.9800
7:76540135:A:AC	donor_gain	0.9800
7:76540136:C:CC	donor_gain	0.9800
7:76534049:T:TA	donor_gain	0.9700
7:76534127:C:CT	acceptor_gain	0.9700
7:76536258:C:CC	acceptor_gain	0.9700
7:76537487:CCTTA:C	donor_loss	0.9700
7:76537488:CTTA:C	donor_loss	0.9700
7:76537489:TTACC:T	donor_loss	0.9700
7:76537490:TACCT:T	donor_loss	0.9700
7:76537491:A:C	donor_loss	0.9700
7:76537492:C:CA	donor_loss	0.9700

AlphaMissense

2061 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:76537529:G:C	F171L	0.987
7:76537529:G:T	F171L	0.987
7:76537531:A:G	F171L	0.987
7:76538599:G:C	F159L	0.982
7:76538599:G:T	F159L	0.982
7:76538601:A:G	F159L	0.982
7:76536228:G:C	F193L	0.980
7:76536228:G:T	F193L	0.980
7:76536230:A:G	F193L	0.980
7:76534077:T:A	K226N	0.976
7:76534077:T:G	K226N	0.976
7:76537530:A:G	F171S	0.975
7:76537518:T:A	D175V	0.959
7:76536180:G:C	F209L	0.956
7:76536180:G:T	F209L	0.956
7:76536182:A:G	F209L	0.956
7:76537518:T:G	D175A	0.956
7:76533721:C:A	W304C	0.955
7:76533721:C:G	W304C	0.955
7:76538600:A:G	F159S	0.955
7:76537497:T:A	D182V	0.954
7:76536229:A:G	F193S	0.948
7:76533723:A:G	W304R	0.946
7:76533723:A:T	W304R	0.946
7:76536183:G:C	F208L	0.944
7:76536183:G:T	F208L	0.944
7:76536185:A:G	F208L	0.944
7:76537519:C:G	D175H	0.943
7:76534111:G:T	A215D	0.939
7:76538591:A:G	L162P	0.936

dbSNP variants (sampled 300 via entrez): RS1000178082 (7:76540152 G>A), RS1000783455 (7:76543766 A>G), RS1001132258 (7:76544177 A>C,G), RS1003640822 (7:76535604 C>G), RS1004035718 (7:76536838 T>C), RS1004627594 (7:76543238 A>C), RS1005048811 (7:76541484 A>G), RS1005634306 (7:76545211 AAG>A), RS1007188426 (7:76541382 G>T), RS1007479386 (7:76534630 C>T), RS1007489451 (7:76532883 A>C), RS1008490320 (7:76541052 C>A,T), RS1009485028 (7:76545005 C>G), RS1009494431 (7:76544249 GA>G), RS1012299982 (7:76540058 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

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance	1
Arsenic	decreases expression, increases abundance	1
Cadmium	decreases expression, increases abundance	1
Cadmium Chloride	decreases expression, increases abundance	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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