U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    Rnf6 ring finger protein (C3H2C3 type) 6 [ Mus musculus (house mouse) ]

    Gene ID: 74132, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Rnf6provided by MGI
    Official Full Name
    ring finger protein (C3H2C3 type) 6provided by MGI
    Primary source
    MGI:MGI:1921382
    See related
    Ensembl:ENSMUSG00000029634 AllianceGenome:MGI:1921382
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    1200013I08Rik; 5730419H05Rik
    Summary
    Enables DNA binding activity and ubiquitin protein ligase activity. Involved in protein K48-linked ubiquitination and ubiquitin-dependent protein catabolic process. Acts upstream of or within negative regulation of axon extension and positive regulation of DNA-templated transcription. Located in PML body; axon; and cytoplasm. Is expressed in central nervous system and genitourinary system. Human ortholog(s) of this gene implicated in esophagus squamous cell carcinoma and squamous cell carcinoma. Orthologous to human RNF6 (ring finger protein 6). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in bladder adult (RPKM 14.8), cerebellum adult (RPKM 13.4) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Rnf6 in Genome Data Viewer
    Location:
    5 G3; 5 85.18 cM
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (146146003..146158267, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (146209193..146221457, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1700001J03 gene Neighboring gene cytochrome P450, family 3, subfamily a, member 60, pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E4806 Neighboring gene predicted gene, 38745 Neighboring gene cyclin dependent kinase 8

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. QKI degradation in macrophage by RNF6 protects mice from MRSA infection via enhancing PI3K p110β dependent autophagy. Zhai D, et al. Cell Biosci, 2022 Sep 10. PMID 36088389, Free PMC Article
    2. Gene control in germinal differentiation: RNF6, a transcription regulatory protein in the mouse sertoli cell. Lopez P, et al. Mol Cell Biol, 2002 May. PMID 11971979, Free PMC Article
    3. Distinct gene loci control the host response to influenza H1N1 virus infection in a time-dependent manner. Nedelko T, et al. BMC Genomics, 2012 Aug 20. PMID 22905720, Free PMC Article
    4. The ubiquitin ligase Rnf6 regulates local LIM kinase 1 levels in axonal growth cones. Tursun B, et al. Genes Dev, 2005 Oct 1. PMID 16204183, Free PMC Article
    5. Accumulation of NCOA1 dependent on HERC3 deficiency transactivates matrix metallopeptidases and promotes extracellular matrix degradation in intervertebral disc degeneration. Li X, et al. Life Sci, 2023 May 1. PMID 36878279

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nuclear androgen receptor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables nuclear androgen receptor 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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of axon extension IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of axon extension IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of axon extension IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of axon extension IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K27-linked ubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K27-linked ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein K48-linked ubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein K6-linked ubiquitination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein K6-linked ubiquitination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of androgen receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of androgen receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in axon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    E3 ubiquitin-protein ligase RNF6
    Names
    RING-type E3 ubiquitin transferase RNF6
    RLIM-like protein
    NP_001243014.1
    NP_001243015.1
    NP_001243016.1
    NP_083050.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001256085.1 → NP_001243014.1  E3 ubiquitin-protein ligase RNF6 isoform 1

      See identical proteins and their annotated locations for NP_001243014.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1-3 encode the same isoform (1).
      Source sequence(s)
      AK004745, AK150269, AV586321, BY136428
      Consensus CDS
      CCDS19868.1
      UniProtKB/Swiss-Prot
      B2RRR0, Q8K565, Q9DBU5
      Related
      ENSMUSP00000067559.4, ENSMUST00000067837.10
      Conserved Domains (1) summary
      pfam13639
      Location:614 → 655
      zf-RING_2; Ring finger domain

    2. NM_001256086.1 → NP_001243015.1  E3 ubiquitin-protein ligase RNF6 isoform 2

      See identical proteins and their annotated locations for NP_001243015.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding region which includes an upstream in-frame AUG start codon, compared to variant 1. The resulting isoform (2) is longer at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AC113316
      Conserved Domains (1) summary
      pfam13639
      Location:625 → 666
      zf-RING_2; Ring finger domain

    3. NM_001256087.1 → NP_001243016.1  E3 ubiquitin-protein ligase RNF6 isoform 1

      See identical proteins and their annotated locations for NP_001243016.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1-3 encode the same isoform (1).
      Source sequence(s)
      AK004745, AV586321, CX237430
      Consensus CDS
      CCDS19868.1
      UniProtKB/Swiss-Prot
      B2RRR0, Q8K565, Q9DBU5
      Related
      ENSMUSP00000128774.3, ENSMUST00000169407.9
      Conserved Domains (1) summary
      pfam13639
      Location:614 → 655
      zf-RING_2; Ring finger domain

    4. NM_028774.3 → NP_083050.1  E3 ubiquitin-protein ligase RNF6 isoform 1

      See identical proteins and their annotated locations for NP_083050.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the predominant isoform (1).
      Source sequence(s)
      AK004745, AV586321, BY323318
      Consensus CDS
      CCDS19868.1
      UniProtKB/Swiss-Prot
      B2RRR0, Q8K565, Q9DBU5
      Related
      ENSMUSP00000124293.2, ENSMUST00000161859.8
      Conserved Domains (1) summary
      pfam13639
      Location:614 → 655
      zf-RING_2; Ring finger domain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000071.7 Reference GRCm39 C57BL/6J

      Range
      146146003..146158267 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9DBU5.1 GenPept UniProtKB/Swiss-Prot:Q9DBU5

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous