RNF180 ring finger protein 180 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RNF180provided by HGNC
Official Full Name: ring finger protein 180provided by HGNC
Primary source: HGNC:HGNC:27752
See related: Ensembl:ENSG00000164197 MIM:616015; AllianceGenome:HGNC:27752
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
Also known as: RINES
Summary: Predicted to enable ubiquitin conjugating enzyme binding activity and ubiquitin protein ligase activity. Predicted to be involved in norepinephrine metabolic process; positive regulation of proteasomal ubiquitin-dependent protein catabolic process; and serotonin metabolic process. Predicted to act upstream of or within several processes, including adult behavior; positive regulation of protein ubiquitination; and protein polyubiquitination. Predicted to be located in nuclear envelope. Predicted to be integral component of membrane. Predicted to be intrinsic component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in thyroid (RPKM 3.9), brain (RPKM 2.6) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q12.3

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (64165351..64372869)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (64985947..65192972)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (63461670..63668696)

Chromosome 5 - NC_000005.10 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?

DNMT3A-mediated silence in ADAMTS9 expression is restored by RNF180 to inhibit viability and motility in gastric cancer cells.
Title: DNMT3A-mediated silence in ADAMTS9 expression is restored by RNF180 to inhibit viability and motility in gastric cancer cells.
RNF180 mediates STAT3 activity by regulating the expression of RhoC via the proteasomal pathway in gastric cancer cells.
Title: RNF180 mediates STAT3 activity by regulating the expression of RhoC via the proteasomal pathway in gastric cancer cells.
relationships between RNF180 promoter methylation and gastric cancer or atrophic gastritis, and the effects of Helicobactor pylori (H.pylori) infection on RNF180 promoter methylation
Title: Promoter methylation of RNF180 is associated with H.pylori infection and serves as a marker for gastric cancer and atrophic gastritis.
The methylated status of the key CpG islands of RNF180 DNA promoter may be used to predict the variations of the malignant biological characteristics of gastric cancer cells.
Title: Mediation of the malignant biological characteristics of gastric cancer cells by the methylated CpG islands in RNF180 DNA promoter.
RNF180 is capable of inhibiting lymph node metastasis of gastric cancer by suppressing the intracellular activation of malignant molecular signals.
Title: Clinical and experimental role of ring finger protein 180 on lymph node metastasis and survival in gastric cancer.
hypermethylated CpG site count of E3 ubiquitin ligase Ring finger protein 180 promoter for evaluating the prognosis of gastric cancer was reasonable by using the direct bisulfite sequencing.
Title: Evaluating the clinical feasibility: The direct bisulfite genomic sequencing for examination of methylated status of E3 ubiquitin ligase RNF180 DNA promoter to predict the survival of gastric cancer.
We found that only few methylated CpG sites of RNF180 promoter was appropriate to predict the survival of gastric cancer
Title: Methylation of CpG sites in RNF180 DNA promoter prediction poor survival of gastric cancer.
Data indicate that the ring finger protein 180 (RNF180) and HTR1A showed association to T1D in the Swedish and Danish families.
Title: HTR1A a novel type 1 diabetes susceptibility gene on chromosome 5p13-q13.
RNF180 is a novel potential tumor suppressor in gastric carcinogenesis.
Title: Characterization of the gene structure, functional significance, and clinical application of RNF180, a novel gene in gastric cancer.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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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

NoName (e-PCR)
- UniSTS:484629

SHGC-30782 (e-PCR)
- UniSTS:77392

D5S668 (e-PCR)
- UniSTS:50116

SHGC-34946 (e-PCR)
- UniSTS:17626

WI-14912 (e-PCR)
- UniSTS:61424

RH92875 (e-PCR)
- UniSTS:88318

Homology

Homologs of the RNF180 gene: The RNF180 gene is conserved in Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 321 organisms have orthologs with human gene RNF180
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin conjugating enzyme binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Process	Evidence Code	Pubs
involved_in adult behavior	IEA Inferred from Electronic Annotation more info
involved_in norepinephrine metabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of proteasomal ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein polyubiquitination	IEA Inferred from Electronic Annotation more info
involved_in regulation of catalytic activity	IEA Inferred from Electronic Annotation more info
involved_in serotonin metabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in nuclear envelope	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase RNF180

Names: RING-type E3 ubiquitin transferase RNF180

NP_001107033.1

EC 2.3.2.27

NP_001310220.1

EC 2.3.2.27

NP_001310221.1

EC 2.3.2.27

NP_848627.1

EC 2.3.2.27

XP_016864872.1

EC 2.3.2.27

XP_016864875.1

EC 2.3.2.27

XP_016864876.1

EC 2.3.2.27

XP_016864877.1

EC 2.3.2.27

XP_016864878.1

EC 2.3.2.27

XP_047273072.1

EC 2.3.2.27

XP_047273074.1

EC 2.3.2.27

XP_047273075.1

EC 2.3.2.27

XP_047273076.1

EC 2.3.2.27

XP_047273077.1

EC 2.3.2.27

XP_047273078.1

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_001113561.2 → NP_001107033.1 E3 ubiquitin-protein ligase RNF180 isoform 1

See identical proteins and their annotated locations for NP_001107033.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AL832580, DA183707, DA809479

Consensus CDS

CCDS47219.1

UniProtKB/Swiss-Prot

Q86T96, Q8NBD1

Related

ENSP00000373752.4, ENST00000389100.9

Conserved Domains (1) summary

cd16554
Location:431 → 474

RING-HC_RNF180; RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins
NM_001323291.1 → NP_001310220.1 E3 ubiquitin-protein ligase RNF180 isoform 3

Status: VALIDATED

Source sequence(s)

AC092360, AK090756, BC101279, DA183707

UniProtKB/Swiss-Prot

Q86T96
NM_001323292.2 → NP_001310221.1 E3 ubiquitin-protein ligase RNF180 isoform 4

Status: VALIDATED

Source sequence(s)

AC016623, AL832580, BC101397, DA183707, DA809479

UniProtKB/Swiss-Prot

Q86T96
NM_178532.4 → NP_848627.1 E3 ubiquitin-protein ligase RNF180 isoform 2

See identical proteins and their annotated locations for NP_848627.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks multiple 3' coding exons and differs in the 3' UTR, compared to variant 1. The resulting isoform (2) has a shorter, distinct C-terminus compared to isoform 1.

Source sequence(s)

AC092360, AK090756, BC101277, DA183707

Consensus CDS

CCDS34169.1

UniProtKB/Swiss-Prot

Q86T96

Related

ENSP00000296615.6, ENST00000296615.10

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

64165351..64372869

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047417118.1 → XP_047273074.1 E3 ubiquitin-protein ligase RNF180 isoform X1
XM_047417120.1 → XP_047273076.1 E3 ubiquitin-protein ligase RNF180 isoform X5

UniProtKB/Swiss-Prot

Q8NBD1
XM_017009388.2 → XP_016864877.1 E3 ubiquitin-protein ligase RNF180 isoform X1
XM_047417119.1 → XP_047273075.1 E3 ubiquitin-protein ligase RNF180 isoform X5

UniProtKB/Swiss-Prot

Q8NBD1
XM_017009383.2 → XP_016864872.1 E3 ubiquitin-protein ligase RNF180 isoform X1
XM_017009386.3 → XP_016864875.1 E3 ubiquitin-protein ligase RNF180 isoform X2
XM_047417116.1 → XP_047273072.1 E3 ubiquitin-protein ligase RNF180 isoform X3
XM_017009387.1 → XP_016864876.1 E3 ubiquitin-protein ligase RNF180 isoform X4
XM_047417121.1 → XP_047273077.1 E3 ubiquitin-protein ligase RNF180 isoform X5

UniProtKB/Swiss-Prot

Q8NBD1
XM_047417122.1 → XP_047273078.1 E3 ubiquitin-protein ligase RNF180 isoform X3
XM_017009389.2 → XP_016864878.1 E3 ubiquitin-protein ligase RNF180 isoform X1