Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	58190
Gene name	CTD small phosphatase 1
Gene symbol	CTDSP1
Synonyms (NCBI Gene)	NIF3NLI-IFNLIIFSCP1
Chromosome	2
Chromosome location	2q35
Summary	This gene encodes a member of the small C-terminal domain phosphatase (SCP) family of nuclear phosphatases. These proteins play a role in transcriptional regulation through specific dephosphorylation of phosphoserine 5 within tandem heptapeptide repeats o

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miRTarBase ID	miRNA	Experiments	Reference
MIRT002729	hsa-miR-124-3p	Microarray	15685193
MIRT022103	hsa-miR-128-3p	Reporter assay	17403776
MIRT002729	hsa-miR-124-3p	Microarray	18668037
MIRT002729	hsa-miR-124-3p	Reporter assay	17403776
MIRT002729	hsa-miR-124-3p	Microarray	15685193
MIRT025925	hsa-miR-7-5p	Microarray	19073608
MIRT030562	hsa-miR-24-3p	Microarray	19748357
MIRT045998	hsa-miR-125b-5p	CLASH	23622248
MIRT002729	hsa-miR-124-3p	PAR-CLIP	20371350
MIRT567877	hsa-miR-4694-3p	PAR-CLIP	20371350
MIRT567876	hsa-miR-224-3p	PAR-CLIP	20371350
MIRT567875	hsa-miR-522-3p	PAR-CLIP	20371350
MIRT567874	hsa-miR-4753-5p	PAR-CLIP	20371350
MIRT567873	hsa-miR-4717-5p	PAR-CLIP	20371350
MIRT352247	hsa-miR-3919	PAR-CLIP	20371350
MIRT407440	hsa-miR-605-3p	PAR-CLIP	20371350
MIRT567872	hsa-miR-4493	PAR-CLIP	20371350
MIRT407443	hsa-miR-6770-5p	PAR-CLIP	20371350
MIRT407441	hsa-miR-4747-5p	PAR-CLIP	20371350
MIRT407442	hsa-miR-5196-5p	PAR-CLIP	20371350
MIRT002729	hsa-miR-124-3p	PAR-CLIP	20371350
MIRT567877	hsa-miR-4694-3p	PAR-CLIP	20371350
MIRT567876	hsa-miR-224-3p	PAR-CLIP	20371350
MIRT567875	hsa-miR-522-3p	PAR-CLIP	20371350
MIRT567874	hsa-miR-4753-5p	PAR-CLIP	20371350
MIRT567873	hsa-miR-4717-5p	PAR-CLIP	20371350
MIRT352247	hsa-miR-3919	PAR-CLIP	20371350
MIRT407440	hsa-miR-605-3p	PAR-CLIP	20371350
MIRT567872	hsa-miR-4493	PAR-CLIP	20371350
MIRT407443	hsa-miR-6770-5p	PAR-CLIP	20371350
MIRT407441	hsa-miR-4747-5p	PAR-CLIP	20371350
MIRT407442	hsa-miR-5196-5p	PAR-CLIP	20371350
MIRT756438	hsa-miR-574-5p	Luciferase reporter assayqRT-PCR	36311195
MIRT914103	hsa-miR-1343	CLIP-seq
MIRT914104	hsa-miR-3192	CLIP-seq
MIRT914105	hsa-miR-3689a-3p	CLIP-seq
MIRT914106	hsa-miR-3689c	CLIP-seq
MIRT914107	hsa-miR-3689d	CLIP-seq
MIRT914108	hsa-miR-4728-5p	CLIP-seq
MIRT914109	hsa-miR-765	CLIP-seq
MIRT914110	hsa-miR-103a	CLIP-seq
MIRT914111	hsa-miR-107	CLIP-seq
MIRT914112	hsa-miR-124	CLIP-seq
MIRT914113	hsa-miR-1252	CLIP-seq
MIRT914114	hsa-miR-1972	CLIP-seq
MIRT914115	hsa-miR-2392	CLIP-seq
MIRT914116	hsa-miR-3158-3p	CLIP-seq
MIRT914117	hsa-miR-3173-3p	CLIP-seq
MIRT914118	hsa-miR-3612	CLIP-seq
MIRT914119	hsa-miR-3622a-3p	CLIP-seq
MIRT914120	hsa-miR-3622b-3p	CLIP-seq
MIRT914121	hsa-miR-4264	CLIP-seq
MIRT914122	hsa-miR-4274	CLIP-seq
MIRT914123	hsa-miR-4446-3p	CLIP-seq
MIRT914124	hsa-miR-4495	CLIP-seq
MIRT914125	hsa-miR-4519	CLIP-seq
MIRT914126	hsa-miR-4520a-3p	CLIP-seq
MIRT914127	hsa-miR-4695-5p	CLIP-seq
MIRT914128	hsa-miR-4704-3p	CLIP-seq
MIRT914129	hsa-miR-4704-5p	CLIP-seq
MIRT914130	hsa-miR-4797-3p	CLIP-seq
MIRT914131	hsa-miR-506	CLIP-seq
MIRT914132	hsa-miR-522	CLIP-seq
MIRT914133	hsa-miR-548c-3p	CLIP-seq
MIRT914134	hsa-miR-650	CLIP-seq
MIRT914110	hsa-miR-103a	CLIP-seq
MIRT914111	hsa-miR-107	CLIP-seq
MIRT914135	hsa-miR-1207-5p	CLIP-seq
MIRT914112	hsa-miR-124	CLIP-seq
MIRT914136	hsa-miR-1255a	CLIP-seq
MIRT914137	hsa-miR-1255b	CLIP-seq
MIRT914138	hsa-miR-1271	CLIP-seq
MIRT914139	hsa-miR-1273e	CLIP-seq
MIRT914140	hsa-miR-1275	CLIP-seq
MIRT914141	hsa-miR-1322	CLIP-seq
MIRT914142	hsa-miR-15a	CLIP-seq
MIRT914143	hsa-miR-15b	CLIP-seq
MIRT914144	hsa-miR-16	CLIP-seq
MIRT914145	hsa-miR-182	CLIP-seq
MIRT914146	hsa-miR-195	CLIP-seq
MIRT914147	hsa-miR-214	CLIP-seq
MIRT914148	hsa-miR-296-5p	CLIP-seq
MIRT914149	hsa-miR-298	CLIP-seq
MIRT914150	hsa-miR-3136-3p	CLIP-seq
MIRT914151	hsa-miR-3179	CLIP-seq
MIRT914152	hsa-miR-3202	CLIP-seq
MIRT914153	hsa-miR-361-3p	CLIP-seq
MIRT914154	hsa-miR-3619-5p	CLIP-seq
MIRT914155	hsa-miR-3714	CLIP-seq
MIRT914156	hsa-miR-3910	CLIP-seq
MIRT914157	hsa-miR-3940-5p	CLIP-seq
MIRT914158	hsa-miR-424	CLIP-seq
MIRT914159	hsa-miR-4271	CLIP-seq
MIRT914122	hsa-miR-4274	CLIP-seq
MIRT914160	hsa-miR-4317	CLIP-seq
MIRT914161	hsa-miR-4462	CLIP-seq
MIRT914162	hsa-miR-4464	CLIP-seq
MIRT914163	hsa-miR-4492	CLIP-seq
MIRT914124	hsa-miR-4495	CLIP-seq
MIRT914164	hsa-miR-4498	CLIP-seq
MIRT914165	hsa-miR-4507	CLIP-seq
MIRT914166	hsa-miR-4508	CLIP-seq
MIRT914167	hsa-miR-4514	CLIP-seq
MIRT914125	hsa-miR-4519	CLIP-seq
MIRT914126	hsa-miR-4520a-3p	CLIP-seq
MIRT914168	hsa-miR-4525	CLIP-seq
MIRT914169	hsa-miR-4532	CLIP-seq
MIRT914170	hsa-miR-4649-3p	CLIP-seq
MIRT914171	hsa-miR-4665-5p	CLIP-seq
MIRT914172	hsa-miR-4690-5p	CLIP-seq
MIRT914173	hsa-miR-4692	CLIP-seq
MIRT914174	hsa-miR-4723-5p	CLIP-seq
MIRT914175	hsa-miR-4725-3p	CLIP-seq
MIRT914176	hsa-miR-4726-3p	CLIP-seq
MIRT914177	hsa-miR-4748	CLIP-seq
MIRT914178	hsa-miR-4763-3p	CLIP-seq
MIRT914179	hsa-miR-494	CLIP-seq
MIRT914180	hsa-miR-497	CLIP-seq
MIRT914131	hsa-miR-506	CLIP-seq
MIRT914133	hsa-miR-548c-3p	CLIP-seq
MIRT914181	hsa-miR-602	CLIP-seq
MIRT914182	hsa-miR-616	CLIP-seq
MIRT914183	hsa-miR-625	CLIP-seq
MIRT914184	hsa-miR-761	CLIP-seq
MIRT914185	hsa-miR-762	CLIP-seq
MIRT914186	hsa-miR-885-3p	CLIP-seq
MIRT914187	hsa-miR-922	CLIP-seq
MIRT914188	hsa-miR-939	CLIP-seq
MIRT914189	hsa-miR-940	CLIP-seq
MIRT914190	hsa-miR-96	CLIP-seq
MIRT1556209	hsa-miR-4456	CLIP-seq
MIRT1556209	hsa-miR-4456	CLIP-seq
MIRT914112	hsa-miR-124	CLIP-seq
MIRT914138	hsa-miR-1271	CLIP-seq
MIRT1971122	hsa-miR-183	CLIP-seq
MIRT1971123	hsa-miR-4453	CLIP-seq
MIRT1556209	hsa-miR-4456	CLIP-seq
MIRT1971124	hsa-miR-4538	CLIP-seq
MIRT914131	hsa-miR-506	CLIP-seq
MIRT756438	hsa-miR-574-5p	CLIP-seq
MIRT914190	hsa-miR-96	CLIP-seq
MIRT914112	hsa-miR-124	CLIP-seq
MIRT914131	hsa-miR-506	CLIP-seq
MIRT914112	hsa-miR-124	CLIP-seq
MIRT1971122	hsa-miR-183	CLIP-seq
MIRT2206796	hsa-miR-2964a-5p	CLIP-seq
MIRT1556209	hsa-miR-4456	CLIP-seq
MIRT914161	hsa-miR-4462	CLIP-seq
MIRT2206797	hsa-miR-4687-5p	CLIP-seq
MIRT914131	hsa-miR-506	CLIP-seq
MIRT914181	hsa-miR-602	CLIP-seq
MIRT914186	hsa-miR-885-3p	CLIP-seq
MIRT914135	hsa-miR-1207-5p	CLIP-seq
MIRT914112	hsa-miR-124	CLIP-seq
MIRT2206798	hsa-miR-1254	CLIP-seq
MIRT2206799	hsa-miR-1285	CLIP-seq
MIRT2206800	hsa-miR-148a	CLIP-seq
MIRT2206801	hsa-miR-148b	CLIP-seq
MIRT2206802	hsa-miR-152	CLIP-seq
MIRT2206803	hsa-miR-18a	CLIP-seq
MIRT2206804	hsa-miR-18b	CLIP-seq
MIRT2206805	hsa-miR-1909	CLIP-seq
MIRT2206806	hsa-miR-1913	CLIP-seq
MIRT2206807	hsa-miR-3116	CLIP-seq
MIRT2206808	hsa-miR-3151	CLIP-seq
MIRT2206809	hsa-miR-3187-5p	CLIP-seq
MIRT2206810	hsa-miR-324-3p	CLIP-seq
MIRT914119	hsa-miR-3622a-3p	CLIP-seq
MIRT914120	hsa-miR-3622b-3p	CLIP-seq
MIRT2206811	hsa-miR-3670	CLIP-seq
MIRT914107	hsa-miR-3689d	CLIP-seq
MIRT2206812	hsa-miR-370	CLIP-seq
MIRT914155	hsa-miR-3714	CLIP-seq
MIRT2206813	hsa-miR-3907	CLIP-seq
MIRT2206814	hsa-miR-3944-5p	CLIP-seq
MIRT2206815	hsa-miR-4254	CLIP-seq
MIRT1971123	hsa-miR-4453	CLIP-seq
MIRT914161	hsa-miR-4462	CLIP-seq
MIRT1971124	hsa-miR-4538	CLIP-seq
MIRT2206816	hsa-miR-4633-3p	CLIP-seq
MIRT914174	hsa-miR-4723-5p	CLIP-seq
MIRT2206817	hsa-miR-4735-3p	CLIP-seq
MIRT2206818	hsa-miR-4749-3p	CLIP-seq
MIRT914178	hsa-miR-4763-3p	CLIP-seq
MIRT2206819	hsa-miR-486-3p	CLIP-seq
MIRT914131	hsa-miR-506	CLIP-seq
MIRT914132	hsa-miR-522	CLIP-seq
MIRT2206820	hsa-miR-596	CLIP-seq
MIRT914181	hsa-miR-602	CLIP-seq
MIRT2206821	hsa-miR-612	CLIP-seq
MIRT914109	hsa-miR-765	CLIP-seq
MIRT914186	hsa-miR-885-3p	CLIP-seq
MIRT914189	hsa-miR-940	CLIP-seq
MIRT914112	hsa-miR-124	CLIP-seq
MIRT914151	hsa-miR-3179	CLIP-seq
MIRT914152	hsa-miR-3202	CLIP-seq
MIRT914153	hsa-miR-361-3p	CLIP-seq
MIRT914155	hsa-miR-3714	CLIP-seq
MIRT914159	hsa-miR-4271	CLIP-seq
MIRT1971123	hsa-miR-4453	CLIP-seq
MIRT914161	hsa-miR-4462	CLIP-seq
MIRT1971124	hsa-miR-4538	CLIP-seq
MIRT914175	hsa-miR-4725-3p	CLIP-seq
MIRT914131	hsa-miR-506	CLIP-seq
MIRT914132	hsa-miR-522	CLIP-seq
MIRT914181	hsa-miR-602	CLIP-seq
MIRT2386553	hsa-miR-637	CLIP-seq
MIRT914189	hsa-miR-940	CLIP-seq
MIRT914112	hsa-miR-124	CLIP-seq
MIRT914131	hsa-miR-506	CLIP-seq
MIRT2510117	hsa-miR-1245b-5p	CLIP-seq
MIRT2510118	hsa-miR-192	CLIP-seq
MIRT2510119	hsa-miR-215	CLIP-seq
MIRT2510120	hsa-miR-3142	CLIP-seq
MIRT2510121	hsa-miR-3175	CLIP-seq
MIRT2510122	hsa-miR-3922-5p	CLIP-seq

Show/Hide all (19)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004721	Function	Phosphoprotein phosphatase activity	IEA
GO:0004722	Function	Protein serine/threonine phosphatase activity	IEA
GO:0005515	Function	Protein binding	IPI	12721286, 16189514, 16882717, 21653829, 25416956, 27880917, 28514442, 31515488, 32296183, 33961781
GO:0005634	Component	Nucleus	IDA	12721286
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	10967134
GO:0005654	Component	Nucleoplasm	IDA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IDA	12721286
GO:0006470	Process	Protein dephosphorylation	IDA	12721286
GO:0008420	Function	RNA polymerase II CTD heptapeptide repeat phosphatase activity	IBA
GO:0008420	Function	RNA polymerase II CTD heptapeptide repeat phosphatase activity	IDA	12721286
GO:0008420	Function	RNA polymerase II CTD heptapeptide repeat phosphatase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016791	Function	Phosphatase activity	IEA
GO:0045665	Process	Negative regulation of neuron differentiation	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050768	Process	Negative regulation of neurogenesis	IEA
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:2000134	Process	Negative regulation of G1/S transition of mitotic cell cycle	IEA

MIM	HGNC	e!Ensembl
605323	21614	ENSG00000144579

Q9GZU7

Protein name

Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 (EC 3.1.3.16) (Nuclear LIM interactor-interacting factor 3) (NLI-IF) (NLI-interacting factor 3) (Small C-terminal domain phosphatase 1) (SCP1) (Small CTD phosphatase 1)

Protein function

Preferentially catalyzes the dephosphorylation of 'Ser-5' within the tandem 7 residue repeats in the C-terminal domain (CTD) of the largest RNA polymerase II subunit POLR2A. Negatively regulates RNA polymerase II transcription, possibly by contr

PDB

1T9Z , 1TA0 , 2GHQ , 2GHT , 3L0B , 3L0C , 3L0Y , 3PGL , 4YGY , 4YH1 , 6DU3

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03031	NIF	91 → 251	NLI interacting factor-like phosphatase	Family

Tissue specificity

TISSUE SPECIFICITY: Expression is restricted to non-neuronal tissues. Highest expression in skeletal muscle, spleen, lung and placenta. {ECO:0000269|PubMed:15681389}.

Sequence

MDSSAVITQISKEEARGPLRGKGDQKSAASQKPRSRGILHSLFCCVCRDDGEALPAHSGA
PLLVEENGAIPKQTPVQYLLPEAKAQDSDKICVVIDLDETLVHSSFKPVNNADFIIPVEI
DGVVHQVYVLKRPHVDEFLQRMGELFECVLFTASLAKYADPVADLLDKWGAFRARLFRES
CVFHRGNYVKDLSRLGRDLRRVLILDNSPASYVFHPDNAVPVASWFDNMSDTELHDLLPF
FEQLSRVDDVYSVLRQPRPGS

Sequence length

261

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
AMYOTROPHIC LATERAL SCLEROSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (8)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Breast Neoplasms	Associate	26975371	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Associate	31774910, 37629167	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Non Small Cell Lung	Associate	31774910	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Associate	37629167	★★★★★ ★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Associate	33147338	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liposarcoma	Associate	31831742	★★★★★ ★☆☆☆☆ Found in Text Mining only
Myelodysplastic Syndromes	Associate	33147338	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Inhibit	26975371	★★★★★ ★☆☆☆☆ Found in Text Mining only

CTDSP1 (CTD small phosphatase 1)