RNF169 ring finger protein 169 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RNF169provided by HGNC
Official Full Name: ring finger protein 169provided by HGNC
Primary source: HGNC:HGNC:26961
See related: Ensembl:ENSG00000166439 MIM:618650; AllianceGenome:HGNC:26961
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: Enables K63-linked polyubiquitin modification-dependent protein binding activity; nucleosome binding activity; and ubiquitin-modified histone reader activity. Involved in double-strand break repair via homologous recombination and negative regulation of double-strand break repair. Located in cytosol; nuclear lumen; and site of double-strand break. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in esophagus (RPKM 6.7), bone marrow (RPKM 6.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.4

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (74748849..74842413)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (74678364..74771928)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (74459894..74553458)

Chromosome 11 - NC_000011.10 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?

A comprehensive proteomics-based interaction screen that links DYRK1A to RNF169 and to the DNA damage response.
Title: A comprehensive proteomics-based interaction screen that links DYRK1A to RNF169 and to the DNA damage response.
results highlight the interplay of RNF169 with 53BP1 in fine-tuning choice of DSB repair pathways.
Title: RNF169 limits 53BP1 deposition at DSBs to stimulate single-strand annealing repair.
USP7 is RNF169 interacting protein.Expression of USP7 and RNF169 positively correlated in breast cancer.
Title: Dual-utility NLS drives RNF169-dependent DNA damage responses.
The authors establish that RNF169 binds to ubiquitylated histone H2A-Lys13/Lys15 in a manner that involves its canonical ubiquitin-binding helix and a pair of arginine-rich motifs that interact with the nucleosome acidic patch.
Title: The RNF168 paralog RNF169 defines a new class of ubiquitylated histone reader involved in the response to DNA damage.
Ubiquitin ligases RNF168, RNF169, and RAD18 specifically bind histone H2A Lys13/15-ubiquitylated nucleosomes. 53BP1 chromatin recruitment may be activated by RNF168 and blocked by RNF169 and RAD18.
Title: Mechanisms of Ubiquitin-Nucleosome Recognition and Regulation of 53BP1 Chromatin Recruitment by RNF168/169 and RAD18.
RNF169 as a component in DNA damage signal transduction and adds to the complexity of regulatory ubiquitylation in genome stability maintenance.
Title: Ring finger protein RNF169 antagonizes the ubiquitin-dependent signaling cascade at sites of DNA damage.
RNF168, its paralog RNF169, RAD18, and the BRCA1-interacting RAP80 protein accumulate at DNA double strand break sites through the use of bipartite modules composed of ubiquitin binding domains.
Title: Tandem protein interaction modules organize the ubiquitin-dependent response to DNA double-strand breaks.
results show that RNF169 functions in a noncanonical fashion to harness RNF168-mediated protein recruitment to DSB-containing chromatin, thereby contributing to regulation of DSB repair pathway utilization.
Title: Human RNF169 is a negative regulator of the ubiquitin-dependent response to DNA double-strand breaks.

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Phenotypes

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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

RH17472 (e-PCR)
- UniSTS:16652

WI-17967 (e-PCR)
- UniSTS:4365

D11S2255E (e-PCR)
- UniSTS:13326

REN21910 (e-PCR)
- UniSTS:346710

STS-R11335 (e-PCR)
- UniSTS:66907

D11S3966 (e-PCR)
- UniSTS:67240

SGC34365 (e-PCR)
- UniSTS:58542

RH35834 (e-PCR)
- UniSTS:436

SGC38235 (e-PCR)
- UniSTS:69051

RH45943 (e-PCR)
- UniSTS:69052

RH18485 (e-PCR)
- UniSTS:71391

D11S2458 (e-PCR)
- UniSTS:3555

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables K63-linked polyubiquitin modification-dependent protein binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleosome binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleosome binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin-modified histone reader activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-protein transferase activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in DNA damage response	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA damage response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in double-strand break repair via homologous recombination	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of double-strand break repair	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of double-strand break repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
is_active_in site of double-strand break	IBA Inferred from Biological aspect of Ancestor more info
located_in site of double-strand break	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: E3 ubiquitin-protein ligase RNF169

Names: RING-type E3 ubiquitin transferase RNF169

NP_001092108.1

EC 2.3.2.27

XP_011543191.1

EC 2.3.2.27

XP_047282663.1

EC 2.3.2.27

XP_054224274.1

EC 2.3.2.27

XP_054224275.1

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_001098638.2 → NP_001092108.1 E3 ubiquitin-protein ligase RNF169

See identical proteins and their annotated locations for NP_001092108.1

Status: VALIDATED

Source sequence(s)

AB082522, AP000560, BU735906

Consensus CDS

CCDS41691.1

UniProtKB/Swiss-Prot

Q6N015, Q8NCN4

Related

ENSP00000299563.4, ENST00000299563.5

Conserved Domains (1) summary

cd00162
Location:68 → 108

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 ...

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_000011.10 Reference GRCh38.p14 Primary Assembly

Range

74748849..74842413

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011544889.4 → XP_011543191.1 E3 ubiquitin-protein ligase RNF169 isoform X1

Conserved Domains (1) summary

cd00162
Location:68 → 108

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 ...
XM_047426707.1 → XP_047282663.1 E3 ubiquitin-protein ligase RNF169 isoform X2