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

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	9646
Gene name	CTR9 component of Paf1/RNA polymerase II complex
Gene symbol	CTR9
Synonyms (NCBI Gene)	SH2BP1TSBPp150p150TSP
Chromosome	11
Chromosome location	11p15.4
Summary	The protein encoded by this gene is a component of the PAF1 complex, which associates with RNA polymerase II and functions in transcriptional regulation and elongation. This complex also plays a role in the modification of histones. [provided by RefSeq, O

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miRTarBase ID	miRNA	Experiments	Reference
MIRT027343	hsa-miR-101-3p	Sequencing	20371350
MIRT031221	hsa-miR-19b-3p	Sequencing	20371350
MIRT052333	hsa-let-7b-5p	CLASH	23622248
MIRT050526	hsa-miR-20a-5p	CLASH	23622248
MIRT050110	hsa-miR-26a-5p	CLASH	23622248
MIRT2207245	hsa-miR-1251	CLIP-seq
MIRT2207246	hsa-miR-1269	CLIP-seq
MIRT2207247	hsa-miR-1269b	CLIP-seq
MIRT2207248	hsa-miR-186	CLIP-seq
MIRT2207249	hsa-miR-217	CLIP-seq
MIRT2207250	hsa-miR-219-2-3p	CLIP-seq
MIRT2207251	hsa-miR-23a	CLIP-seq
MIRT2207252	hsa-miR-23b	CLIP-seq
MIRT2207253	hsa-miR-23c	CLIP-seq
MIRT2207254	hsa-miR-3143	CLIP-seq
MIRT2207255	hsa-miR-3671	CLIP-seq
MIRT2207256	hsa-miR-4260	CLIP-seq
MIRT2207257	hsa-miR-4283	CLIP-seq
MIRT2207258	hsa-miR-4328	CLIP-seq
MIRT2207259	hsa-miR-4418	CLIP-seq
MIRT2207260	hsa-miR-4489	CLIP-seq
MIRT2207261	hsa-miR-4529-3p	CLIP-seq
MIRT2207262	hsa-miR-4704-5p	CLIP-seq
MIRT2207263	hsa-miR-4803	CLIP-seq
MIRT2207264	hsa-miR-509-3-5p	CLIP-seq
MIRT2207265	hsa-miR-509-5p	CLIP-seq
MIRT2207266	hsa-miR-5096	CLIP-seq
MIRT2207267	hsa-miR-593	CLIP-seq
MIRT2207268	hsa-miR-635	CLIP-seq
MIRT2207269	hsa-miR-639	CLIP-seq
MIRT2510302	hsa-miR-101	CLIP-seq
MIRT2510303	hsa-miR-105	CLIP-seq
MIRT2510304	hsa-miR-1238	CLIP-seq
MIRT2510305	hsa-miR-143	CLIP-seq
MIRT2510306	hsa-miR-144	CLIP-seq
MIRT2207249	hsa-miR-217	CLIP-seq
MIRT2207251	hsa-miR-23a	CLIP-seq
MIRT2207252	hsa-miR-23b	CLIP-seq
MIRT2207253	hsa-miR-23c	CLIP-seq
MIRT2510307	hsa-miR-3064-3p	CLIP-seq
MIRT2510308	hsa-miR-3647-3p	CLIP-seq
MIRT2510309	hsa-miR-3653	CLIP-seq
MIRT2510310	hsa-miR-3658	CLIP-seq
MIRT2510311	hsa-miR-3667-3p	CLIP-seq
MIRT2207255	hsa-miR-3671	CLIP-seq
MIRT2510312	hsa-miR-3674	CLIP-seq
MIRT2510313	hsa-miR-3675-3p	CLIP-seq
MIRT2510314	hsa-miR-3935	CLIP-seq
MIRT2510315	hsa-miR-4282	CLIP-seq
MIRT2510316	hsa-miR-4297	CLIP-seq
MIRT2207258	hsa-miR-4328	CLIP-seq
MIRT2207259	hsa-miR-4418	CLIP-seq
MIRT2510317	hsa-miR-4528	CLIP-seq
MIRT2510318	hsa-miR-4691-5p	CLIP-seq
MIRT2510319	hsa-miR-4704-3p	CLIP-seq
MIRT2207262	hsa-miR-4704-5p	CLIP-seq
MIRT2510320	hsa-miR-4756-3p	CLIP-seq
MIRT2510321	hsa-miR-4770	CLIP-seq
MIRT2510322	hsa-miR-4789-5p	CLIP-seq
MIRT2510323	hsa-miR-494	CLIP-seq
MIRT2207264	hsa-miR-509-3-5p	CLIP-seq
MIRT2207265	hsa-miR-509-5p	CLIP-seq
MIRT2207266	hsa-miR-5096	CLIP-seq
MIRT2510324	hsa-miR-513a-3p	CLIP-seq
MIRT2510325	hsa-miR-513b	CLIP-seq
MIRT2510326	hsa-miR-520a-5p	CLIP-seq
MIRT2510327	hsa-miR-525-5p	CLIP-seq
MIRT2510328	hsa-miR-548c-3p	CLIP-seq
MIRT2510329	hsa-miR-561	CLIP-seq
MIRT2510330	hsa-miR-570	CLIP-seq
MIRT2510331	hsa-miR-607	CLIP-seq
MIRT2510332	hsa-miR-629	CLIP-seq
MIRT2207269	hsa-miR-639	CLIP-seq
MIRT2510333	hsa-miR-656	CLIP-seq
MIRT2510334	hsa-miR-758	CLIP-seq
MIRT2510335	hsa-miR-9	CLIP-seq
MIRT2510336	hsa-miR-936	CLIP-seq
MIRT2510302	hsa-miR-101	CLIP-seq
MIRT2510303	hsa-miR-105	CLIP-seq
MIRT2510306	hsa-miR-144	CLIP-seq
MIRT2510308	hsa-miR-3647-3p	CLIP-seq
MIRT2510309	hsa-miR-3653	CLIP-seq
MIRT2510310	hsa-miR-3658	CLIP-seq
MIRT2510311	hsa-miR-3667-3p	CLIP-seq
MIRT2207255	hsa-miR-3671	CLIP-seq
MIRT2510313	hsa-miR-3675-3p	CLIP-seq
MIRT2510314	hsa-miR-3935	CLIP-seq
MIRT2510315	hsa-miR-4282	CLIP-seq
MIRT2510316	hsa-miR-4297	CLIP-seq
MIRT2510317	hsa-miR-4528	CLIP-seq
MIRT2207262	hsa-miR-4704-5p	CLIP-seq
MIRT2510322	hsa-miR-4789-5p	CLIP-seq
MIRT2510324	hsa-miR-513a-3p	CLIP-seq
MIRT2510330	hsa-miR-570	CLIP-seq
MIRT2510331	hsa-miR-607	CLIP-seq
MIRT2207269	hsa-miR-639	CLIP-seq
MIRT2510334	hsa-miR-758	CLIP-seq
MIRT2510335	hsa-miR-9	CLIP-seq
MIRT2510336	hsa-miR-936	CLIP-seq

Show/Hide all (37)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	ISS
GO:0000791	Component	Euchromatin	IEA
GO:0000791	Component	Euchromatin	ISS
GO:0000993	Function	RNA polymerase II complex binding	IBA
GO:0001711	Process	Endodermal cell fate commitment	IEA
GO:0001711	Process	Endodermal cell fate commitment	ISS
GO:0001826	Process	Inner cell mass cell differentiation	IEA
GO:0001829	Process	Trophectodermal cell differentiation	IEA
GO:0001832	Process	Blastocyst growth	IEA
GO:0001835	Process	Blastocyst hatching	IEA
GO:0005515	Function	Protein binding	IPI	15923622, 16024656, 19136632, 19410543, 20178742, 20541477, 24981860, 26030138, 26496610, 28514442, 29774127, 33961781, 34819669
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0006325	Process	Chromatin organization	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0006368	Process	Transcription elongation by RNA polymerase II	IBA
GO:0006368	Process	Transcription elongation by RNA polymerase II	IDA	20178742
GO:0007259	Process	Cell surface receptor signaling pathway via JAK-STAT	IEA
GO:0007259	Process	Cell surface receptor signaling pathway via JAK-STAT	ISS
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0016593	Component	Cdc73/Paf1 complex	IBA
GO:0016593	Component	Cdc73/Paf1 complex	IDA	16307923, 20178742
GO:0016593	Component	Cdc73/Paf1 complex	IEA
GO:0016607	Component	Nuclear speck	IEA
GO:0019827	Process	Stem cell population maintenance	IDA	19345177
GO:0019827	Process	Stem cell population maintenance	IEA
GO:0042169	Function	SH2 domain binding	IEA
GO:0045638	Process	Negative regulation of myeloid cell differentiation	IDA	20541477
GO:0045814	Process	Negative regulation of gene expression, epigenetic	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	16307923
GO:0070102	Process	Interleukin-6-mediated signaling pathway	IEA
GO:0070102	Process	Interleukin-6-mediated signaling pathway	ISS
GO:0071222	Process	Cellular response to lipopolysaccharide	IEA
GO:0071222	Process	Cellular response to lipopolysaccharide	ISS

MIM	HGNC	e!Ensembl
609366	16850	ENSG00000198730

Q6PD62

Protein name

RNA polymerase-associated protein CTR9 homolog (SH2 domain-binding protein 1)

Protein function

Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase

PDB

5ZYQ , 6GMH , 6TED , 7OOP , 7OPC , 7OPD , 7UNC , 7UND , 8A3Y , 9EGX , 9EGY , 9EGZ , 9EH0 , 9EH1 , 9EH2

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13181	TPR_8	451 → 484	Tetratricopeptide repeat	Repeat
PF13176	TPR_7	499 → 529	Tetratricopeptide repeat	Repeat
PF13181	TPR_8	681 → 709	Tetratricopeptide repeat	Repeat

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:8590280}.

Sequence

MSRGSIEIPLRDTDEVIELDFDQLPEGDEVISILKQEHTQLHIWIALALEYYKQGKTEEF
VKLLEAARIDGNLDYRDHEKDQMTCLDTLAAYYVQQARKEKNKDNKKDLITQATLLYTMA
DKIIMYDQNHLLGRACFCLLEGDKMDQADAQFHFVLNQSPNNIPALLGKACISFNKKDYR
GALAYYKKALRTNPGCPAEVRLGMGHCFVKLNKLEKARLAFSRALELNSKCVGALVGLAV
LELNNKEADSIKNGVQLLSRAYTIDPSNPMVLNHLANHFFFKKDYSKVQHLALHAFHNTE
VEAMQAESCYQLARSFHVQEDYDQAFQYYYQATQFASSSFVLPFFGLGQMYIYRGDKENA
SQCFEKVLKAYPNNYETMKILGSLYAASEDQEKRDIAKGHLKKVTEQYPDDVEAWIELAQ
ILEQTDIQGALSAYGTATRILQEKVQADVPPEILNNVGALHFRLGNLGEAKKYFLASLDR
AKAEAEHDEHYYNAISVTTSYNLARLYEAMCEFHEAEKLYKNILREHPNYVDCYLRLGAM
ARDKGNFYEASDWFKEALQINQDHPDAWSLIGNLHLAKQEWGPGQKKFERILKQPSTQSD
TYSMLALGNVWLQTLHQPTRDREKEKRHQDRALAIYKQVLRNDAKNLYAANGIGAVLAHK
GYFREARDVFAQVREATADISDVWLNLAHIYVEQKQYISAVQMYENCLRKFYKHQNTEVV
LYLARALFKCGKLQECKQTLLKARHVAPSDTVLMFNVALVLQRLATSVLKDEKSNLKEVL
NAVKELELAHRYFSYLSKVGDKMRFDLALAATEARQCSDLLSQAQYHVARARKQDEEERE
LRAKQEQEKELLRQKLLKEQEEKRLREKEEQKKLLEQRAQYVEKTKNILMFTGETEATKE
KKRGGGGGRRSKKGGEFDEFVNDDTDDDLPISKKKKRRKGSGSEQEGEDEEGGERKKKKR
RRHPKGEEGSDDDETENGPKPKKRRPPKAEKKKAPKPERLPPSMKGKIKSKAIISSSDDS
SDEDKLKIADEGHPRNSNSNSDSDEDEQRKKCASSESDSDENQNKSGSEAGSPRRPRRQR
SDQDSDSDQPSRKRRPSGSEQSDNESVQSGRSHSGVSENDSRPASPSAESDHESERGSDN
EGSGQGSGNESEPEGSNNEASDRGSEHGSDDSD

Sequence length

1173

Interactions

View interactions

	Reactome
			Formation of RNA Pol II elongation complex RNA Polymerase II Pre-transcription Events RNA Polymerase II Transcription Elongation E3 ubiquitin ligases ubiquitinate target proteins

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 Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
CTR9-related neurodevelopmental disorder	Likely pathogenic; Pathogenic	rs2135351445, rs2135353090, rs2135353126, rs2135353143, rs2135353178, rs2135356050, rs772196842, rs2135369472, rs1397467879	RCV001796986 RCV001796988 RCV001796994 RCV001796991 RCV001796987 RCV001796990 RCV001796992 RCV001796989 RCV001796995	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodevelopmental disorder	Likely pathogenic; Pathogenic	rs2135353090	RCV006249756	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (17)

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.
Acute myeloid leukemia	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHILDHOOD KIDNEY WILMS TUMOR	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CTR9-related disorder	Conflicting classifications of pathogenicity; Likely benign; Benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALIGNANT EPITHELIAL TUMOR OF OVARY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-SPECIFIC SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Predisposition to Wilms tumor	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Predisposition to Wilms tumor, CTR9-related	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (20)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Ataxia	Associate	35499524	★★★★★ ★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorder	Associate	35499524	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Body Dysmorphic Disorders	Associate	35499524	★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Associate	26494790, 27829357, 35137163	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Non Small Cell Lung	Associate	35961388	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colitis Collagenous	Associate	33930606	★★★★★ ★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Associate	28209224	★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Associate	35499524	★★★★★ ★☆☆☆☆ Found in Text Mining only
Granulomatous Mastitis	Associate	39201744	★★★★★ ★☆☆☆☆ Found in Text Mining only
Heart Diseases	Associate	35499524	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hematologic Neoplasms	Associate	38218188	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hereditary Breast and Ovarian Cancer Syndrome	Associate	26494790	★★★★★ ★☆☆☆☆ Found in Text Mining only
Inflammation	Associate	28355295	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Associate	35499524	★★★★★ ★☆☆☆☆ Found in Text Mining only
Language Development Disorders	Associate	35499524	★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscle Hypotonia	Associate	35499524	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	25099282, 35137163, 38218188	★★★★★ ★☆☆☆☆ Found in Text Mining only
Tremor	Associate	35499524	★★★★★ ★☆☆☆☆ Found in Text Mining only
Tuberculosis Pulmonary	Associate	28355295	★★★★★ ★☆☆☆☆ Found in Text Mining only
Wilms Tumor	Associate	25099282, 39293508, 40340749	★★★★★ ★☆☆☆☆ Found in Text Mining only

CTR9 (CTR9 component of Paf1/RNA polymerase II complex)