RNF4 ring finger protein 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RNF4provided by HGNC
Official Full Name: ring finger protein 4provided by HGNC
Primary source: HGNC:HGNC:10067
See related: Ensembl:ENSG00000063978 MIM:602850; AllianceGenome:HGNC:10067
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: SLX5; SNURF; RES4-26
Summary: The protein encoded by this gene contains a RING finger motif and acts as a transcription regulator. This protein has been shown to interact with, and inhibit the activity of, TRPS1, a transcription suppressor of GATA-mediated transcription. Transcription repressor ZNF278/PATZ is found to interact with this protein, and thus reduce the enhancement of androgen receptor-dependent transcription mediated by this protein. Studies of the mouse and rat counterparts suggested a role of this protein in spermatogenesis. A pseudogene of this gene is found on chromosome 1.[provided by RefSeq, Jul 2010]
Expression: Ubiquitous expression in lymph node (RPKM 20.6), testis (RPKM 19.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4p16.3

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (2469106..2515857)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (2467864..2514631)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (2470833..2517584)

Chromosome 4 - NC_000004.12 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: 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?

Nuclear p62 condensates stabilize the promyelocytic leukemia nuclear bodies by sequestering their ubiquitin ligase RNF4.
Title: Nuclear p62 condensates stabilize the promyelocytic leukemia nuclear bodies by sequestering their ubiquitin ligase RNF4.
RNF4 sustains Myc-driven tumorigenesis by facilitating DNA replication.
Title: RNF4 sustains Myc-driven tumorigenesis by facilitating DNA replication.
RNF4 prevents genomic instability caused by chronic DNA under-replication.
Title: RNF4 prevents genomic instability caused by chronic DNA under-replication.
RNF4~RGMb~BMP6 axis required for osteogenic differentiation and cancer cell survival.
Title: RNF4~RGMb~BMP6 axis required for osteogenic differentiation and cancer cell survival.
RNF4 promotes tumorigenesis, therapy resistance of cholangiocarcinoma and affects cell cycle by regulating the ubiquitination degradation of p27kip1 in the nucleus.
Title: RNF4 promotes tumorigenesis, therapy resistance of cholangiocarcinoma and affects cell cycle by regulating the ubiquitination degradation of p27kip1 in the nucleus.
PRMT5-mediated RNF4 methylation promotes therapeutic resistance of APL cells to As2O3 by stabilizing oncoprotein PML-RARalpha.
Title: PRMT5-mediated RNF4 methylation promotes therapeutic resistance of APL cells to As(2)O(3) by stabilizing oncoprotein PML-RARα.
RNF4 silencing induces cell growth arrest and DNA damage by promoting nuclear targeting of p62 in hepatocellular carcinoma.
Title: RNF4 silencing induces cell growth arrest and DNA damage by promoting nuclear targeting of p62 in hepatocellular carcinoma.
Roles of the SUMO-related enzymes, PIAS1, PIAS4, and RNF4, in DNA double-strand break repair by homologous recombination.
Title: Roles of the SUMO-related enzymes, PIAS1, PIAS4, and RNF4, in DNA double-strand break repair by homologous recombination.
Knockdown of endogenous RNF4 exacerbates ischaemia-induced cardiomyocyte apoptosis in mice.
Title: Knockdown of endogenous RNF4 exacerbates ischaemia-induced cardiomyocyte apoptosis in mice.
Regulation of eIF2alpha by RNF4 Promotes Melanoma Tumorigenesis and Therapy Resistance.
Title: Regulation of eIF2α by RNF4 Promotes Melanoma Tumorigenesis and Therapy Resistance.

Submit: New GeneRIF Correction See all GeneRIFs (55)

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

GDB:434012 (e-PCR)
- UniSTS:157204

RH64743 (e-PCR)
- UniSTS:91457

RH64880 (e-PCR)
- UniSTS:87623

Cda0fc06 (e-PCR)
- UniSTS:27995

RH65312 (e-PCR)
- UniSTS:92518

D4S2764E (e-PCR)
- UniSTS:153744

D4S816E (e-PCR)
- UniSTS:473016

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables SUMO polymer binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables nuclear receptor coactivator activity	TAS Traceable Author Statement more info	PubMed
enables nucleosome binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	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 activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in negative regulation of protein localization to chromatin	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein K11-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein K48-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein K6-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein K63-linked ubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein autoubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of kinetochore assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of spindle assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to arsenic-containing substance	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
colocalizes_with PML body	IBA Inferred from Biological aspect of Ancestor more info
colocalizes_with PML body	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in microtubule end	IDA Inferred from Direct Assay more info
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: E3 ubiquitin-protein ligase RNF4

Names: E3 ubiquitin ligase RNF4; RING-type E3 ubiquitin transferase RNF4; small nuclear RING finger protein

NP_001171938.1

EC 2.3.2.27

NP_001171939.1

EC 2.3.2.27

NP_002929.1

EC 2.3.2.27

XP_047272018.1

EC 2.3.2.27

XP_054206669.1

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_001185009.3 → NP_001171938.1 E3 ubiquitin-protein ligase RNF4 isoform 1

See identical proteins and their annotated locations for NP_001171938.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Both variants 1 and 2 encode the same isoform (2).

Source sequence(s)

AB000468, BC031935, BX322586, DB064628, U95140

Consensus CDS

CCDS47001.1

UniProtKB/Swiss-Prot

B2R6D6, D6RF58, P78317, Q49AR8

UniProtKB/TrEMBL

D6RA71

Related

ENSP00000424076.1, ENST00000506706.5

Conserved Domains (1) summary

cd16533
Location:127 → 180

RING-HC_RNF4; RING finger, HC subclass, found in RING finger protein 4 (RNF4) and similar proteins
NM_001185010.3 → NP_001171939.1 E3 ubiquitin-protein ligase RNF4 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate exon in the 3' coding region which results in a frameshift, compared to variant 1. The resulting protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AB000468, AK309509, BX322586, DA342512, U95140

Consensus CDS

CCDS54713.1

UniProtKB/TrEMBL

D6RAD8

Related

ENSP00000446369.2, ENST00000541204.5
NM_002938.5 → NP_002929.1 E3 ubiquitin-protein ligase RNF4 isoform 1

See identical proteins and their annotated locations for NP_002929.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (2).

Source sequence(s)

AB000468, BX322586, DA342512, U95140

Consensus CDS

CCDS47001.1

UniProtKB/Swiss-Prot

B2R6D6, D6RF58, P78317, Q49AR8

UniProtKB/TrEMBL

D6RA71

Related

ENSP00000315212.8, ENST00000314289.13

Conserved Domains (1) summary

cd16533
Location:127 → 180

RING-HC_RNF4; RING finger, HC subclass, found in RING finger protein 4 (RNF4) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

2469106..2515857

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047416062.1 → XP_047272018.1 E3 ubiquitin-protein ligase RNF4 isoform X1

UniProtKB/Swiss-Prot

B2R6D6, D6RF58, P78317, Q49AR8

UniProtKB/TrEMBL

D6RA71

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

2467864..2514631

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054350694.1 → XP_054206669.1 E3 ubiquitin-protein ligase RNF4 isoform X1

UniProtKB/Swiss-Prot

B2R6D6, D6RF58, P78317, Q49AR8

UniProtKB/TrEMBL

D6RA71