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RNF5 ring finger protein 5 [ Homo sapiens (human) ]

Gene ID: 6048, updated on 12-Oct-2019

Summary

Official Symbol
RNF5provided by HGNC
Official Full Name
ring finger protein 5provided by HGNC
Primary source
HGNC:HGNC:10068
See related
Ensembl:ENSG00000204308 MIM:602677
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
RMA1; RING5
Summary
The protein encoded by this gene contains a RING finger, which is a motif known to be involved in protein-protein interactions. This protein is a membrane-bound ubiquitin ligase. It can regulate cell motility by targeting paxillin ubiquitination and altering the distribution and localization of paxillin in cytoplasm and cell focal adhesions. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in kidney (RPKM 45.9), small intestine (RPKM 33.9) and 25 other tissues See more
Orthologs

Genomic context

See RNF5 in Genome Data Viewer
Location:
6p21.32
Exon count:
6
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (32178405..32180793)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32146162..32148570)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene PPT2-EGFL8 readthrough (NMD candidate) Neighboring gene EGF like domain multiple 8 Neighboring gene 1-acylglycerol-3-phosphate O-acyltransferase 1 Neighboring gene microRNA 6721 Neighboring gene microRNA 6833 Neighboring gene advanced glycosylation end-product specific receptor Neighboring gene PBX homeobox 2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
NHGRI GWA Catalog
Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of ring finger protein 5, E3 ubiquitin protein ligase (RNF5) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with ring finger protein 5, E3 ubiquitin protein ligase (RNF5) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • ABC transporter disorders, organism-specific biosystem (from REACTOME)
    ABC transporter disorders, organism-specific biosystemThe ATP-binding cassette (ABC) transporters form a large family of transmembrane proteins that utilise the energy from the hydrolysis of ATP to facilitate the movement of a wide variety of substrates...
  • ABC-family proteins mediated transport, organism-specific biosystem (from REACTOME)
    ABC-family proteins mediated transport, organism-specific biosystemThe ATP-binding cassette (ABC) superfamily of active transporters involves a large number of functionally diverse transmembrane proteins. They transport a variety of compounds through membranes agai...
  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • Calnexin/calreticulin cycle, organism-specific biosystem (from REACTOME)
    Calnexin/calreticulin cycle, organism-specific biosystemThe unfolded protein is recognized by a chaperon protein (calnexin or calreticulin) and the folding process starts. The binding of these protein requires a mono-glucosylated glycan (Caramelo JJ and P...
  • Defective CFTR causes cystic fibrosis, organism-specific biosystem (from REACTOME)
    Defective CFTR causes cystic fibrosis, organism-specific biosystemCystic fibrosis transmembrane conductance regulator (CFTR) is a low conductance chloride-selective channel that mediates the transport of chloride ions in human airway epithelial cells. Chloride ions...
  • Disease, organism-specific biosystem (from REACTOME)
    Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
  • Disorders of transmembrane transporters, organism-specific biosystem (from REACTOME)
    Disorders of transmembrane transporters, organism-specific biosystemProteins with transporting functions can be roughly classified into 3 categories: ATP hydrolysis-coupled pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to ...
  • ER Quality Control Compartment (ERQC), organism-specific biosystem (from REACTOME)
    ER Quality Control Compartment (ERQC), organism-specific biosystemProteins that are released from the CNX or CRT complex with folding defects accumulate in a compartment of the ER called ERQC (Kamhi-Nesher et al. 2001). Here, the enzymes UGGG1 or UGGG2 are able to ...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystem (from REACTOME)
    N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystemAfter being synthesized in the ER membrane the 14-sugars lipid-linked oligosaccharide is co-translationally transferred to an unfolded protein, as described in the previous steps. After this point th...
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Protein processing in endoplasmic reticulum, organism-specific biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, organism-specific biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
  • Protein processing in endoplasmic reticulum, conserved biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, conserved biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
  • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
    Transmembrane transport of small molecules, organism-specific biosystem
    Transmembrane transport of small molecules

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase activity TAS
Traceable Author Statement
more info
PubMed 
ubiquitin-like protein conjugating enzyme binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
PubMed 
zinc ion binding TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
ER-associated misfolded protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ER-associated misfolded protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
ERAD pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
endoplasmic reticulum mannose trimming TAS
Traceable Author Statement
more info
 
negative regulation of autophagy IEA
Inferred from Electronic Annotation
more info
 
protein K48-linked ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein K63-linked ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein destabilization IEA
Inferred from Electronic Annotation
more info
 
regulation of autophagosome assembly IEA
Inferred from Electronic Annotation
more info
 
response to bacterium IEA
Inferred from Electronic Annotation
more info
 
transmembrane transport TAS
Traceable Author Statement
more info
 
ubiquitin-dependent ERAD pathway IGI
Inferred from Genetic Interaction
more info
PubMed 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
endoplasmic reticulum quality control compartment IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
mitochondrial membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
E3 ubiquitin-protein ligase RNF5
Names
RING-type E3 ubiquitin transferase RNF5
protein G16
ram1 homolog
ring finger protein 5, E3 ubiquitin protein ligase
NP_008844.1

NCBI Reference Sequences (RefSeq)

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)

  1. NM_006913.4NP_008844.1  E3 ubiquitin-protein ligase RNF5

    See identical proteins and their annotated locations for NP_008844.1

    Status: REVIEWED

    Source sequence(s)
    BC004155, BC127652, BM712189
    Consensus CDS
    CCDS4745.1
    UniProtKB/Swiss-Prot
    Q99942
    UniProtKB/TrEMBL
    A0A024RCQ4
    Related
    ENSP00000364235.3, ENST00000375094.4
    Conserved Domains (2) summary
    cd16743
    Location:2570
    RING-HC_RNF5; RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins
    cl28410
    Location:21116
    RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    32178405..32180793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    3511007..3513395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    3616757..3619145
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    Range
    3483386..3485774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    3520426..3522812
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    3401606..3403994
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    3494612..3497000
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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