Rnf40 ring finger protein 40 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rnf40provided by MGI
Official Full Name: ring finger protein 40provided by MGI
Primary source: MGI:MGI:2142048
See related: Ensembl:ENSMUSG00000030816 AllianceGenome:MGI:2142048
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: BRE1-B; mKIAA0661
Summary: Predicted to enable several functions, including enzyme binding activity; protein homodimerization activity; and syntaxin-1 binding activity. Predicted to be involved in positive regulation of macromolecule metabolic process and ubiquitin-dependent protein catabolic process. Predicted to be located in nucleoplasm. Predicted to be part of HULC complex. Predicted to be active in nucleus. Is expressed in central nervous system; genitourinary system; and islets of Langerhans. Orthologous to human RNF40 (ring finger protein 40). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in testis adult (RPKM 29.9), thymus adult (RPKM 22.4) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 F3; 7 69.61 cM

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (127187936..127202777)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (127588698..127603605)

Chromosome 7 - NC_000073.7 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: Mouse ENCODE transcriptome data 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?

RNF20/RNF40 ameliorates streptozotocin-induced type 1 diabetes by activating vitamin D receptors in vivo.
Title: RNF20/RNF40 ameliorates streptozotocin-induced type 1 diabetes by activating vitamin D receptors in vivo.
RNF40 exerts stage-dependent functions in differentiating osteoblasts and is essential for bone cell crosstalk.
Title: RNF40 exerts stage-dependent functions in differentiating osteoblasts and is essential for bone cell crosstalk.
Massively parallel in vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation.
Title: Massively parallel in vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation.
Rnf40 depletion reduces beta-cell H2Bub1 marks and uncovered several target genes, including glucose transporter 2 (Glut2), MAF BZIP transcription factor A (MafA), and uncoupling protein 2 (Ucp2). RNF40 regulates transcription through imparting monoubiquitin marks on histone H2B (H2Bub1), a precursor to histone H3 lysine 4 trimethylation (H3K4me3).
Title: LIM-domain transcription complexes interact with ring-finger ubiquitin ligases and thereby impact islet β-cell function.
Results suggest that RNF20, RNF40, and H2Bub may represent a novel pathway for DSB sensing and repair.
Title: E3 Ubiquitin Ligases RNF20 and RNF40 Are Required for Double-Stranded Break (DSB) Repair: Evidence for Monoubiquitination of Histone H2B Lysine 120 as a Novel Axis of DSB Signaling and Repair.
Our findings suggest that RNF40 plays a central role in the maintenance of tumorigenic features and inflammatory signaling by promoting nuclear NF-kappaB activity.
Title: Loss of RNF40 Decreases NF-κB Activity in Colorectal Cancer Cells and Reduces Colitis Burden in Mice.
Our results support a model in which the direct function of RNF40-mediated H2B monoubiquitination increases transcriptional elongation by promoting the spreading of H3K4me3 into the 5' transcribed region of a select subgroup of genes.
Title: RNF40 regulates gene expression in an epigenetic context-dependent manner.
We show that Bre1 (human BRE1A/B (RNF20/40) and mouse Bre1a/b (Rnf20/40)) acts as an important suppressor of chromosomal instability
Title: Deficiency in mammalian histone H2B ubiquitin ligase Bre1 (Rnf20/Rnf40) leads to replication stress and chromosomal instability.
the observed defects in the radiation response of Bre1a/b-deficient cells
Title: Deficiency in Bre1 impairs homologous recombination repair and cell cycle checkpoint response to radiation damage in mammalian cells.

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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 (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:235783

NoName (e-PCR)
- UniSTS:492065

AI848422 (e-PCR)
- UniSTS:165557

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables mRNA 3'-UTR binding	IEA Inferred from Electronic Annotation more info
enables mRNA 3'-UTR binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables syntaxin-1 binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin conjugating enzyme binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin-protein transferase activity	IEA Inferred from Electronic Annotation more info
contributes_to ubiquitin-protein transferase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-protein transferase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of proteasomal protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein polyubiquitination	ISO Inferred from Sequence Orthology more info
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 protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-dependent protein catabolic process	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of HULC complex	IBA Inferred from Biological aspect of Ancestor more info
part_of HULC complex	ISO Inferred from Sequence Orthology more info
part_of HULC complex	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of ubiquitin ligase complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase BRE1B

Names: RING-type E3 ubiquitin transferase BRE1B

NP_001347812.1

EC 2.3.2.27

NP_001408710.1

EC 2.3.2.27

NP_001408711.1

EC 2.3.2.27

NP_001408712.1

EC 2.3.2.27

NP_001408713.1

EC 2.3.2.27

NP_758485.2

EC 2.3.2.27

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_001360883.1 → NP_001347812.1 E3 ubiquitin-protein ligase BRE1B isoform 2

Status: VALIDATED

Source sequence(s)

AC122417, BM899169

Conserved Domains (3) summary

cd16815
Location:612 → 666

RING-HC_RNF40; RING finger, HC subclass, found in RING finger protein 40 (RNF40)

cl25732
Location:2 → 608

SMC_N; RecF/RecN/SMC N terminal domain

cl26511
Location:295 → 593

Neuromodulin_N; Gap junction protein N-terminal region
NM_001421781.1 → NP_001408710.1 E3 ubiquitin-protein ligase BRE1B isoform 3

Status: VALIDATED

Source sequence(s)

AC122417
NM_001421782.1 → NP_001408711.1 E3 ubiquitin-protein ligase BRE1B isoform 4

Status: VALIDATED

Source sequence(s)

AC122417
NM_001421783.1 → NP_001408712.1 E3 ubiquitin-protein ligase BRE1B isoform 2

Status: VALIDATED

Source sequence(s)

AC122417
NM_001421784.1 → NP_001408713.1 E3 ubiquitin-protein ligase BRE1B isoform 5

Status: VALIDATED

Source sequence(s)

AC122417
NM_172281.3 → NP_758485.2 E3 ubiquitin-protein ligase BRE1B isoform 1

See identical proteins and their annotated locations for NP_758485.2

Status: VALIDATED

Source sequence(s)

AC122417

Consensus CDS

CCDS21871.1

UniProtKB/Swiss-Prot

Q3U319, Q6ZQ75, Q8BJA1, Q8BY03, Q8CHX4

UniProtKB/TrEMBL

A0A0X1KG60

Related

ENSMUSP00000146310.2, ENSMUST00000205694.2

Conserved Domains (3) summary

cd00162
Location:947 → 990

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

TIGR02168
Location:200 → 946

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam08647
Location:754 → 848

BRE1; BRE1 E3 ubiquitin ligase