RNF40 ring finger protein 40 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RNF40provided by HGNC
Official Full Name: ring finger protein 40provided by HGNC
Primary source: HGNC:HGNC:16867
See related: Ensembl:ENSG00000103549 MIM:607700; AllianceGenome:HGNC:16867
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: BRE1B; RBP95; STARING
Summary: The protein encoded by this gene contains a RING finger, a motif known to be involved in protein-protein and protein-DNA interactions. This protein was reported to interact with the tumor suppressor protein RB1. Studies of the rat counterpart suggested that this protein may function as an E3 ubiquitin-protein ligase, and facilitate the ubiquitination and degradation of syntaxin 1, which is an essential component of the neurotransmitter release machinery. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]
Expression: Ubiquitous expression in testis (RPKM 21.6), bone marrow (RPKM 14.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p11.2

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (30761612..30776307)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (31149033..31163750)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (30772933..30787628)

Chromosome 16 - NC_000016.10 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RNF40 epigenetically modulates glycolysis to support the aggressiveness of basal-like breast cancer.
Title: RNF40 epigenetically modulates glycolysis to support the aggressiveness of basal-like breast cancer.
Epigenetic modification and a role for the E3 ligase RNF40 in cancer development and metastasis.
Title: Epigenetic modification and a role for the E3 ligase RNF40 in cancer development and metastasis.
The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis.
Title: The histone H2B ubiquitin ligase RNF40 is required for HER2-driven mammary tumorigenesis.
The H2B ubiquitin-protein ligase RNF40 is required for somatic cell reprogramming.
Title: The H2B ubiquitin-protein ligase RNF40 is required for somatic cell reprogramming.
The RNF20/40 complex regulates p53-dependent gene transcription and mRNA splicing.
Title: The RNF20/40 complex regulates p53-dependent gene transcription and mRNA splicing.
Findings reveal that RNF40 is essential for maintaining tumorigenic features of colorectal cancer cells in vitro by controlling the expression of genes encoding central apoptotic regulators.
Title: The E3 ubiquitin ligase RNF40 suppresses apoptosis in colorectal cancer cells.
Cooperative physical interactions among eEF1BdeltaL, RNF20/40, and HSF1 synergistically promote expression of heat shock-responsive genes. In addition, eEF1BdeltaL is a novel ubiquitylation target of RNF20/40 and elucidating its function. This provides a molecular mechanism for the cooperative function of distinct transcription factors in heat shock-responsive gene transcription.
Title: RNF20/40-mediated eEF1BδL monoubiquitylation stimulates transcription of heat shock-responsive genes.
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.
the RNF20/40 complex, a major ubiquitin ligase catalysing histone H2B monoubiquitination, interacts with the motor protein Eg5 during mitosis and participates in spindle assembly.
Title: Ubiquitin ligase RNF20/40 facilitates spindle assembly and promotes breast carcinogenesis through stabilizing motor protein Eg5.
The authors also show that the RING domains of RNF20 and RNF40 can form a stable heterodimer that is active.
Title: Structure and Function of the RING Domains of RNF20 and RNF40, Dimeric E3 Ligases that Monoubiquitylate Histone H2B.

Submit: New GeneRIF Correction See all GeneRIFs (18)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH65200 (e-PCR)
- UniSTS:85053

RH103172 (e-PCR)
- UniSTS:97505

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables mRNA 3'-UTR binding	IDA Inferred from Direct Assay more info	PubMed
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	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed
contributes_to ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
NOT involved_in regulation of mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of HULC complex	IBA Inferred from Biological aspect of Ancestor more info
part_of HULC complex	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of ubiquitin ligase complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: E3 ubiquitin-protein ligase BRE1B

Names: 95 kDa retinoblastoma protein binding protein; 95 kDa retinoblastoma-associated protein; BRE1 E3 ubiquitin ligase homolog B; BRE1-B; RING-type E3 ubiquitin transferase BRE1B; Rb-associated protein; ring finger protein 40, E3 ubiquitin protein ligase

NP_001193962.1

EC 2.3.2.27

NP_001193963.1

EC 2.3.2.27

NP_001273501.1

EC 2.3.2.27

NP_055586.1

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_001207033.1 → NP_001193962.1 E3 ubiquitin-protein ligase BRE1B isoform 2

See identical proteins and their annotated locations for NP_001193962.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an alternate splice site in the coding region, compared to variant 1. The resulting isoform (2) lacks an internal aa, compared to isoform 1.

Source sequence(s)

AB014561, AC106886, AI373490, AK291666

UniProtKB/TrEMBL

A0A0S2Z537, A8K6K1

Conserved Domains (3) summary

cd00162
Location:946 → 989

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:231 → 945

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam08647
Location:754 → 848

BRE1; BRE1 E3 ubiquitin ligase
NM_001207034.1 → NP_001193963.1 E3 ubiquitin-protein ligase BRE1B isoform 3

See identical proteins and their annotated locations for NP_001193963.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks in-frame two consecutive exons in the coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.

Source sequence(s)

AC106886, AI373490, AK027406, AK291666, BC018647

Consensus CDS

CCDS55994.1

UniProtKB/TrEMBL

H3BP71

Related

ENSP00000350563.5, ENST00000357890.9

Conserved Domains (3) summary

COG1196
Location:193 → 844

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

cd00162
Location:847 → 890

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 ...

pfam08647
Location:654 → 748

BRE1; BRE1 E3 ubiquitin ligase
NM_001286572.3 → NP_001273501.1 E3 ubiquitin-protein ligase BRE1B isoform 1

See identical proteins and their annotated locations for NP_001273501.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1 and 4 both encode the same isoform (1).

Source sequence(s)

AC106886, KF456183

Consensus CDS

CCDS10691.1

UniProtKB/Swiss-Prot

A0A024QZG0, O75150, Q6AHZ6, Q6N005, Q7L3T6, Q8N615, Q96T18, Q9BSV9, Q9HC82

UniProtKB/TrEMBL

A0A0S2Z537

Conserved Domains (2) summary

cd16815
Location:945 → 999

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

cl25732
Location:231 → 920

SMC_N; RecF/RecN/SMC N terminal domain
NM_014771.4 → NP_055586.1 E3 ubiquitin-protein ligase BRE1B isoform 1

See identical proteins and their annotated locations for NP_055586.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 4 both encode the same isoform (1).

Source sequence(s)

AC106886, KF456183

Consensus CDS

CCDS10691.1

UniProtKB/Swiss-Prot

A0A024QZG0, O75150, Q6AHZ6, Q6N005, Q7L3T6, Q8N615, Q96T18, Q9BSV9, Q9HC82

UniProtKB/TrEMBL

A0A0S2Z537

Related

ENSP00000325677.6, ENST00000324685.11

Conserved Domains (2) summary

cd16815
Location:945 → 999

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

cl25732
Location:231 → 920

SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

30761612..30776307

Download

GenBank, FASTA, Sequence Viewer (Graphics)

RNA

XR_007064931.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

31149033..31163750

Download

GenBank, FASTA, Sequence Viewer (Graphics)

RNA

XR_008484755.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_194352.1: Suppressed sequence

Description

NM_194352.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.