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; AllianceGenome:HGNC:16850
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
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Genomic context

Location:: 11p15.4

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (10751246..10779746)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (10836160..10864657)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (10772793..10801293)

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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Inherited blood cancer predisposition through altered transcription elongation.
Title: Inherited blood cancer predisposition through altered transcription elongation.
CTR9 drives osteochondral lineage differentiation of human mesenchymal stem cells via epigenetic regulation of BMP-2 signaling.
Title: CTR9 drives osteochondral lineage differentiation of human mesenchymal stem cells via epigenetic regulation of BMP-2 signaling.
Transcriptional regulator CTR9 promotes hepatocellular carcinoma progression and metastasis via increasing PEG10 transcriptional activity.
Title: Transcriptional regulator CTR9 promotes hepatocellular carcinoma progression and metastasis via increasing PEG10 transcriptional activity.
Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder.
Title: Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder.
The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium.
Title: The transcriptional elongation factor CTR9 demarcates PRC2-mediated H3K27me3 domains by altering PRC2 subtype equilibrium.
MicroRNA-17-3p is upregulated in psoriasis and regulates keratinocyte hyperproliferation and pro-inflammatory cytokine secretion by targeting <em>CTR9</em>.
Title: MicroRNA-17-3p is upregulated in psoriasis and regulates keratinocyte hyperproliferation and pro-inflammatory cytokine secretion by targeting <em>CTR9</em>.
CTR9-mediated JAK2/STAT3 pathway promotes the proliferation, migration, and invasion of human glioma cells.
Title: CTR9-mediated JAK2/STAT3 pathway promotes the proliferation, migration, and invasion of human glioma cells.
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.

Submit: New GeneRIF Correction See all GeneRIFs (17)

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)

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

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

Gene Ontology Provided by GOA

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

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within blastocyst growth	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within blastocyst hatching	IEA Inferred from Electronic Annotation more info
involved_in cell surface receptor signaling pathway via JAK-STAT	IEA Inferred from Electronic Annotation more info
involved_in cell surface receptor signaling pathway via JAK-STAT	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in cellular response to lipopolysaccharide	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in endodermal cell fate commitment	IEA Inferred from Electronic Annotation more info
involved_in endodermal cell fate commitment	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within inner cell mass cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in interleukin-6-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in interleukin-6-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within negative regulation of gene expression, epigenetic	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of myeloid cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in stem cell population maintenance	IDA Inferred from Direct Assay more info	PubMed
involved_in stem cell population maintenance	IEA Inferred from Electronic Annotation more info
involved_in transcription elongation by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription elongation by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within trophectodermal cell differentiation	IEA Inferred from Electronic Annotation more info

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

UniProtKB/TrEMBL

A8K6X9
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

D3DQV8, Q15015, Q6PD62

UniProtKB/TrEMBL

A8K6X9

Related

ENSP00000355013.2, ENST00000361367.7

Conserved Domains (3) summary

TIGR02917
Location:110 → 781

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:501 → 525

TPR; TPR repeat [structural motif]

NF033609
Location:1029 → 1173

MSCRAMM_ClfA; MSCRAMM family adhesin clumping factor ClfA