CTR9 CTR9 homolog, Paf1/RNA polymerase II complex component [Homo sapiens (human)] - Gene

Summary

Official Symbol: CTR9provided by HGNC
Official Full Name: CTR9 homolog, Paf1/RNA polymerase II complex componentprovided by HGNC
Primary source: HGNC:HGNC:16850
See related: Ensembl:ENSG00000198730 MIM:609366
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: TSBP; p150; SH2BP1; p150TSP
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, Oct 2016]
Expression: Ubiquitous expression in testis (RPKM 19.1), thyroid (RPKM 14.8) and 25 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 11p15.4

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
109.20200228	current	GRCh38.p13 (GCF_000001405.39)	11	NC_000011.10 (10751246..10779746)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (10772749..10801295)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study reports 2.53 A atomic structures of both the human PAF1/CTR9 and yeast Paf1/Ctr9 heterodimers. Results clearly reveal that the heterodimer of PAF1/CTR9 or Paf1/Ctr9 is the core component of evolutionarily conserved multifunctional polymerase-associated factor 1 complex (Paf1C) and is important for human PAF1C or yeast Paf1C assembly, yeast viability, and Paf1C-mediated histone modifications.
Title: Paf1 and Ctr9 subcomplex formation is essential for Paf1 complex assembly and functional regulation.
A novel CTR9 germline variant, located in a consensus splice acceptor site, was found to segregate with Wilms tumor in the family.
Title: Identification of a novel CTR9 germline mutation in a family with Wilms tumor.
Our data demonstrated that Ctr9, independent of other PAFc subunits, controls ERalpha-target gene expression by regulating global chromatin occupancies of ERalpha and RNAPII.
Title: Systematic identification of Ctr9 regulome in ERα-positive breast cancer.
Ctr9, a key subunit of hPAFc, is a central regulator of estrogen signaling that drives ERalpha(+) breast tumorigenesis
Title: Ctr9, a key subunit of PAFc, affects global estrogen signaling and drives ERα-positive breast tumorigenesis.
Ctr9, formerly identified as a nuclei protein, interacts with the dopamine transporter in the cytoplasmic compartment.
Title: Ctr9, a Protein in the Transcription Complex Paf1, Regulates Dopamine Transporter Activity at the Plasma Membrane.
CTR9 is a PAF1 complex gene whose germline mutations predispose to Wilms tumour
Title: Germline mutations in the PAF1 complex gene CTR9 predispose to Wilms tumour.
CTR9, a component of PAF complex, controls elongation block at the c-Fos locus via signal-dependent regulation of chromatin-bound NELF dissociation.
Title: CTR9, a component of PAF complex, controls elongation block at the c-Fos locus via signal-dependent regulation of chromatin-bound NELF dissociation.
MLL interacts directly with the polymerase associated factor complex (PAFc) via Paf1 and CTR9. PAFc augments MLL and MLL-AF9 mediated transcriptional activation of Hoxa9 and their interaction is essential for leukemogenesis.
Title: The PAF complex synergizes with MLL fusion proteins at HOX loci to promote leukemogenesis.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: SNP combinations in chromosome-wide genes are associated with bone mineral density in Taiwanese women.
CTR9 participates in the transcription of IL-6-responsive genes through the regulation of DNA association of STAT3 and modification of histone methylation
Title: hCTR9, a component of Paf1 complex, participates in the transcription of interleukin 6-responsive genes through regulation of STAT3-DNA interactions.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) by siRNA enhances the early stages of HIV-1 replication in HeLa-CD4 cells infected with viral pseudotypes HIV89.6R and HIV8.2N	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_17483-17484:1016467358:1 (e-PCR)
- UniSTS:268314

RH93322 (e-PCR)
- UniSTS:24615

CTR9 (e-PCR)
- UniSTS:504150

G62052 (e-PCR)
- UniSTS:139160

RH25374 (e-PCR)
- UniSTS:64667

SHGC-31621 (e-PCR)
- UniSTS:18130

Homology

Homologs of the CTR9 gene: The CTR9 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 311 organisms have orthologs with human gene CTR9
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
RNA polymerase II complex binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
SH2 domain binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
JAK-STAT cascade	ISS Inferred from Sequence or Structural Similarity more info
Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
blastocyst growth	IEA Inferred from Electronic Annotation more info
blastocyst hatching	IEA Inferred from Electronic Annotation more info
cellular response to lipopolysaccharide	ISS Inferred from Sequence or Structural Similarity more info
endodermal cell fate commitment	ISS Inferred from Sequence or Structural Similarity more info
histone H2B ubiquitination	IDA Inferred from Direct Assay more info	PubMed
histone H3-K4 trimethylation	IMP Inferred from Mutant Phenotype more info	PubMed
histone monoubiquitination	IDA Inferred from Direct Assay more info	PubMed
inner cell mass cell differentiation	IEA Inferred from Electronic Annotation more info
interleukin-6-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
negative regulation of mRNA polyadenylation	IMP Inferred from Mutant Phenotype more info	PubMed
negative regulation of myeloid cell differentiation	IDA Inferred from Direct Assay more info	PubMed
negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
positive regulation of histone H2B ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of histone H3-K4 methylation	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of histone H3-K79 methylation	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
positive regulation of transcription elongation from RNA polymerase II promoter	IDA Inferred from Direct Assay more info	PubMed
protein ubiquitination	TAS Traceable Author Statement more info
regulation of genetic imprinting	IEA Inferred from Electronic Annotation more info
regulation of histone H3-K4 methylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
regulation of transcription, DNA-templated	IBA Inferred from Biological aspect of Ancestor more info	PubMed
stem cell population maintenance	IDA Inferred from Direct Assay more info	PubMed
transcription by RNA polymerase II	TAS Traceable Author Statement more info
transcription elongation from RNA polymerase II promoter	TAS Traceable Author Statement more info
trophectodermal cell differentiation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
Cdc73/Paf1 complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
Cdc73/Paf1 complex	IDA Inferred from Direct Assay more info	PubMed
nuclear speck	IEA Inferred from Electronic Annotation more info
nucleoplasm	IDA Inferred from Direct Assay more info
nucleoplasm	TAS Traceable Author Statement more info
transcriptionally active chromatin	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: RNA polymerase-associated protein CTR9 homolog

Names: Ctr9, Paf1/RNA polymerase II complex component, homolog; SH2 domain binding protein 1 (tetratricopeptide repeat containing); TPR-containing, SH2-binding phosphoprotein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_051671.1 RefSeqGene

Range

5260..33760

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001346279.2 → NP_001333208.1 RNA polymerase-associated protein CTR9 homolog isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AC116535
NM_014633.5 → NP_055448.1 RNA polymerase-associated protein CTR9 homolog isoform 1

See identical proteins and their annotated locations for NP_055448.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

BP223102, BP250198, D63875

Consensus CDS

CCDS7805.1

UniProtKB/Swiss-Prot

Q6PD62

Related

ENSP00000355013.2, ENST00000361367.7

Conserved Domains (6) summary

TIGR02795
Location:310 → 420

tol_pal_ybgF; tol-pal system protein YbgF

PHA03249
Location:1034 → 1173

PHA03249; DNA packaging tegument protein UL25; Provisional

sd00006
Location:501 → 525

TPR; TPR repeat [structural motif]

pfam13414
Location:165 → 228

TPR_11; TPR repeat

pfam13424
Location:498 → 563

TPR_12; Tetratricopeptide repeat

pfam14797
Location:1041 → 1154

SEEEED; Serine-rich region of AP3B1, clathrin-adaptor complex