Cbx4 chromobox 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Cbx4provided by RGD
Full Name: chromobox 4provided by RGD
Primary source: RGD:1587243
See related: Ensembl:ENSRNOG00000063043 AllianceGenome:RGD:1587243
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
Summary: Predicted to enable several functions, including SUMO binding activity; SUMO ligase activity; and nucleic acid binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II and protein sumoylation. Predicted to be located in nuclear body. Predicted to be part of PRC1 complex. Human ortholog(s) of this gene implicated in hepatocellular carcinoma. Orthologous to human CBX4 (chromobox 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 147.3), Thymus (RPKM 131.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q32.3

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (104835685..104841727, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (104337140..104343210, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (108190947..108196455, complement)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Chromobox homolog 4 overexpression inhibits TNF-alpha-induced matrix catabolism and senescence by suppressing activation of the NF-kappaB signaling pathway in nucleus pulposus cells.
Title: Chromobox homolog 4 overexpression inhibits TNF-α-induced matrix catabolism and senescence by suppressing activation of the NF-κB signaling pathway in nucleus pulposus cells.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables SUMO binding	IBA Inferred from Biological aspect of Ancestor more info
enables SUMO binding	ISO Inferred from Sequence Orthology more info
enables SUMO ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables SUMO ligase activity	ISO Inferred from Sequence Orthology more info
enables SUMO transferase activity	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables phosphoprotein binding	ISO Inferred from Sequence Orthology more info
enables single-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	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 protein sumoylation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within protein sumoylation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of PRC1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of PRC1 complex	ISO Inferred from Sequence Orthology more info
part_of PcG protein complex	ISO Inferred from Sequence Orthology more info
located_in nuclear body	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: E3 SUMO-protein ligase CBX4

Names: chromobox homolog 4 (Pc class homolog, Drosophila)

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.