Ctr9 CTR9 homolog, Paf1/RNA polymerase II complex component [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ctr9provided by MGI
Official Full Name: CTR9 homolog, Paf1/RNA polymerase II complex componentprovided by MGI
Primary source: MGI:MGI:109345
See related: Ensembl:ENSMUSG00000005609 AllianceGenome:MGI:109345
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Tsp; Tsbp; Sh2bp1; mKIAA0155
Summary: Enables SH2 domain binding activity. Involved in several processes, including cell surface receptor signaling pathway; cellular response to lipopolysaccharide; and endodermal cell fate commitment. Acts upstream of or within blastocyst development and negative regulation of gene expression, epigenetic. Located in euchromatin and nucleus. Part of Cdc73/Paf1 complex. Is expressed in cerebral cortex and telencephalon. Orthologous to human CTR9 (CTR9 homolog, Paf1/RNA polymerase II complex component). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in placenta adult (RPKM 19.3), CNS E11.5 (RPKM 16.4) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 E3; 7 57.98 cM

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (110628158..110655584)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (111028951..111056377)

Chromosome 7 - NC_000073.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

our data suggest that Setd5 is required for maintaining PGC-associated genes and Setd5-associated protein complexes containing Tbl1xr1 and Ctr9, which in turn are likely involved in regulating germ cell-related genes in mESCs
Title: SET domain-containing protein 5 is required for expression of primordial germ cell specification-associated genes in murine embryonic stem cells.
these data propose a novel feed-forward loop of IL-17 transcriptional regulatory circuit, via IL-6-mediated repression of CTR9 which is a transcriptional repressor of IL-17.
Title: Transcriptional regulator CTR9 inhibits Th17 differentiation via repression of IL-17 expression.
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.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (2)

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

RH124844 (e-PCR)
- UniSTS:161666

AI785031 (e-PCR)
- UniSTS:165548

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA polymerase II complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables SH2 domain binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to protein binding	IPI Inferred from Physical Interaction more info	PubMed
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	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within blastocyst growth	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blastocyst hatching	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell surface receptor signaling pathway via JAK-STAT	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to lipopolysaccharide	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endodermal cell fate commitment	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner cell mass cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in interleukin-6-mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression, epigenetic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of myeloid cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myeloid cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in stem cell population maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in stem cell population maintenance	ISO Inferred from Sequence Orthology 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	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within trophectodermal cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

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

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); SH2 domain-binding protein 1; TPR-containing, SH2-binding phosphoprotein of 150 kDa; p150TSP; tetratricopeptide repeat-containing, SH2-binding phosphoprotein of 150 kDa

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.

mRNA and Protein(s)

NM_009431.2 → NP_033457.2 RNA polymerase-associated protein CTR9 homolog

See identical proteins and their annotated locations for NP_033457.2

Status: VALIDATED

Source sequence(s)

AI841408, BC024749, BY012072, L49502

Consensus CDS

CCDS21750.1

UniProtKB/Swiss-Prot

Q3UFF5, Q3UY40, Q62018, Q66JX4, Q7TPS6, Q8BND9, Q8BRD1, Q8C9W7, Q8C9Y3, Q8CHI1

Related

ENSMUSP00000005749.6, ENSMUST00000005749.6

Conserved Domains (6) summary

PHA02664
Location:1051 → 1154

PHA02664; hypothetical protein; Provisional

TIGR02795
Location:310 → 414

tol_pal_ybgF; tol-pal system protein YbgF

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:1039 → 1159

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