Ctr9 CTR9 homolog, Paf1/RNA polymerase II complex component [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ctr9provided by RGD
Official Full Name: CTR9 homolog, Paf1/RNA polymerase II complex componentprovided by RGD
Primary source: RGD:1311097
See related: Ensembl:ENSRNOG00000017195 AllianceGenome:RGD:1311097
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Sh2bp1
Summary: Predicted to enable RNA polymerase II complex binding activity and SH2 domain binding activity. Predicted to be involved in several processes, including histone modification; negative regulation of RNA metabolic process; and positive regulation of histone modification. Predicted to act upstream of or within blastocyst development and regulation of genetic imprinting. Predicted to be located in nucleoplasm and transcriptionally active chromatin. Predicted to be part of Cdc73/Paf1 complex. Orthologous to human CTR9 (CTR9 homolog, Paf1/RNA polymerase II complex component). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 172.0), Thymus (RPKM 158.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q33

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (174571952..174601974)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (165137277..165167303)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (175839140..175869167)

Chromosome 1 - NC_086019.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.

Submit: New GeneRIF Correction

General gene information

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Markers

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

CTR9 (e-PCR)
- UniSTS:504150

RH128530 (e-PCR)
- UniSTS:211838

AI231369 (e-PCR)
- UniSTS:260794

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA polymerase II complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables SH2 domain binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within blastocyst growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within blastocyst hatching	ISO Inferred from Sequence Orthology more info
involved_in cell surface receptor signaling pathway via JAK-STAT	ISO Inferred from Sequence Orthology more info
involved_in cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in chromatin organization	ISO Inferred from Sequence Orthology more info
involved_in endodermal cell fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner cell mass cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in interleukin-6-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of gene expression, epigenetic	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of myeloid cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology 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	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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within trophectodermal cell differentiation	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
part_of euchromatin	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology 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)

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_001100661.1 → NP_001094131.1 RNA polymerase-associated protein CTR9 homolog

See identical proteins and their annotated locations for NP_001094131.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A8I6A0W5, A6I832, G3V897

Related

ENSRNOP00000023741.5, ENSRNOT00000023741.8

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]

NF000535
Location:971 → 1173

MSCRAMM_SdrC; MSCRAMM family adhesin SdrC