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RNF6 ring finger protein 6 [ Homo sapiens (human) ]

Gene ID: 6049, updated on 4-Nov-2018

Summary

Official Symbol
RNF6provided by HGNC
Official Full Name
ring finger protein 6provided by HGNC
Primary source
HGNC:HGNC:10069
See related
Ensembl:ENSG00000127870 MIM:604242; Vega:OTTHUMG00000016614
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
Summary
The protein encoded by this gene contains a RING-H2 finger motif. Deletions and mutations in this gene were detected in esophageal squamous cell carcinoma (ESCC), suggesting that this protein may be a potential tumor suppressor. Studies of the mouse counterpart suggested a role of this protein in the transcription regulation that controls germinal differentiation. Multiple alternatively spliced transcript variants encoding the same protein are observed. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 18.5), brain (RPKM 11.7) and 25 other tissues See more
Orthologs

Genomic context

See RNF6 in Genome Data Viewer
Location:
13q12.13
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 13 NC_000013.11 (26132115..26223085, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (26786894..26796686, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 415 Neighboring gene ATPase phospholipid transporting 8A2 pseudogene 3 Neighboring gene prune exopolyphosphatase pseudogene 1 Neighboring gene THAP domain containing 12 pseudogene 6 Neighboring gene cyclin dependent kinase 8

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Malignant tumor of esophagus
MedGen: C0546837 OMIM: 133239 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A comprehensive genetic association study of Alzheimer disease in African Americans.
NHGRI GWA Catalog
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
NHGRI GWA Catalog

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Androgen receptor signaling pathway, organism-specific biosystem (from WikiPathways)
    Androgen receptor signaling pathway, organism-specific biosystemAndrogens, mainly testosterone and 5alpha-dihydrotestosterone (DHT) play significant role in the growth and development of the male reproductive organs. These steroid hormones bring about their biolo...
  • Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystem (from REACTOME)
    Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystemIntracellular foreign or aberrant host proteins are cleaved into peptide fragments of a precise size, such that they can be loaded on to class I MHC molecules and presented externally to cytotoxic T ...
  • Class I MHC mediated antigen processing & presentation, organism-specific biosystem (from REACTOME)
    Class I MHC mediated antigen processing & presentation, organism-specific biosystemMajor histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular b...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp686P0776

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
androgen receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase activity IEA
Inferred from Electronic Annotation
more info
 
ubiquitin-protein transferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
negative regulation of axon extension ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein K27-linked ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein K48-linked ubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
protein K6-linked ubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
regulation of androgen receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of androgen receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin-dependent protein catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
PML body IEA
Inferred from Electronic Annotation
more info
 
axon ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nuclear membrane IDA
Inferred from Direct Assay
more info
 
nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
E3 ubiquitin-protein ligase RNF6
Names
RING-H2 protein RNF-6
RING-type E3 ubiquitin transferase RNF6
ring finger protein (C3H2C3 type) 6
NP_005968.1
NP_898864.1
NP_898865.1
NP_898866.1
XP_005266542.1
XP_005266543.1
XP_011533479.1
XP_011533480.1
XP_016876174.1
XP_016876175.1
XP_016876176.1
XP_024305158.1
XP_024305159.1
XP_024305160.1

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.

Genomic

  1. NG_017042.2 RefSeqGene

    Range
    5001..14604
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005977.3NP_005968.1  E3 ubiquitin-protein ligase RNF6 isoform 1

    See identical proteins and their annotated locations for NP_005968.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1, 3, and 4 all encode the same isoform (1).
    Source sequence(s)
    AL138966
    Consensus CDS
    CCDS9316.1
    UniProtKB/Swiss-Prot
    Q9Y252
    UniProtKB/TrEMBL
    A0A024RDP2
    Related
    ENSP00000371000.4, OTTHUMP00000018156, ENST00000381588.8, OTTHUMT00000044246
    Conserved Domains (1) summary
    cd16673
    Location:630674
    RING-H2_RNF6; RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins
  2. NM_183043.2NP_898864.1  E3 ubiquitin-protein ligase RNF6 isoform 1

    See identical proteins and their annotated locations for NP_898864.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, as compared to variant 1. Variants 1, 3, and 4 all encode the same isoform (1).
    Source sequence(s)
    AJ010347, AK293272, DC310579
    Consensus CDS
    CCDS9316.1
    UniProtKB/Swiss-Prot
    Q9Y252
    UniProtKB/TrEMBL
    A0A024RDP2
    Related
    ENSP00000342121.3, OTTHUMP00000018154, ENST00000346166.7, OTTHUMT00000044241
    Conserved Domains (1) summary
    cd16673
    Location:630674
    RING-H2_RNF6; RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins
  3. NM_183044.2NP_898865.1  E3 ubiquitin-protein ligase RNF6 isoform 1

    See identical proteins and their annotated locations for NP_898865.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, as compared to variant 1. Variants 1, 3, and 4 all encode the same isoform (1).
    Source sequence(s)
    AY009109, BP310130, BU633523, DB062601
    Consensus CDS
    CCDS9316.1
    UniProtKB/Swiss-Prot
    Q9Y252
    UniProtKB/TrEMBL
    A0A024RDP2
    Related
    ENSP00000370982.3, OTTHUMP00000018155, ENST00000381570.7, OTTHUMT00000044242
    Conserved Domains (1) summary
    cd16673
    Location:630674
    RING-H2_RNF6; RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins
  4. NM_183045.1NP_898866.1  E3 ubiquitin-protein ligase RNF6 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AF293342, BI461269
    UniProtKB/Swiss-Prot
    Q9Y252

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p12 Primary Assembly

    Range
    26132115..26223085 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535178.2XP_011533480.1  E3 ubiquitin-protein ligase RNF6 isoform X3

    See identical proteins and their annotated locations for XP_011533480.1

    UniProtKB/Swiss-Prot
    Q9Y252
  2. XM_024449392.1XP_024305160.1  E3 ubiquitin-protein ligase RNF6 isoform X2

  3. XM_024449390.1XP_024305158.1  E3 ubiquitin-protein ligase RNF6 isoform X1

    Conserved Domains (1) summary
    cd16673
    Location:630674
    RING-H2_RNF6; RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins
  4. XM_017020686.1XP_016876175.1  E3 ubiquitin-protein ligase RNF6 isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z4G9
  5. XM_005266485.3XP_005266542.1  E3 ubiquitin-protein ligase RNF6 isoform X1

    See identical proteins and their annotated locations for XP_005266542.1

    UniProtKB/Swiss-Prot
    Q9Y252
    UniProtKB/TrEMBL
    A0A024RDP2
    Conserved Domains (1) summary
    cd16673
    Location:630674
    RING-H2_RNF6; RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins
  6. XM_011535177.3XP_011533479.1  E3 ubiquitin-protein ligase RNF6 isoform X1

    See identical proteins and their annotated locations for XP_011533479.1

    UniProtKB/Swiss-Prot
    Q9Y252
    UniProtKB/TrEMBL
    A0A024RDP2
    Conserved Domains (1) summary
    cd16673
    Location:630674
    RING-H2_RNF6; RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins
  7. XM_017020685.2XP_016876174.1  E3 ubiquitin-protein ligase RNF6 isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z4G9
  8. XM_017020687.1XP_016876176.1  E3 ubiquitin-protein ligase RNF6 isoform X2

    UniProtKB/TrEMBL
    A0A0S2Z4G9
  9. XM_005266486.2XP_005266543.1  E3 ubiquitin-protein ligase RNF6 isoform X1

    See identical proteins and their annotated locations for XP_005266543.1

    UniProtKB/Swiss-Prot
    Q9Y252
    UniProtKB/TrEMBL
    A0A024RDP2
    Conserved Domains (1) summary
    cd16673
    Location:630674
    RING-H2_RNF6; RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins
  10. XM_024449391.1XP_024305159.1  E3 ubiquitin-protein ligase RNF6 isoform X2

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