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    RNF31 ring finger protein 31 [ Homo sapiens (human) ]

    Gene ID: 55072, updated on 28-Oct-2024

    Summary

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    Official Symbol
    RNF31provided by HGNC
    Official Full Name
    ring finger protein 31provided by HGNC
    Primary source
    HGNC:HGNC:16031
    See related
    Ensembl:ENSG00000092098 MIM:612487; AllianceGenome:HGNC:16031
    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
    HOIP; Paul; ZIBRA; IMD115
    Summary
    The protein encoded by this gene contains a RING finger, a motif present in a variety of functionally distinct proteins and known to be involved in protein-DNA and protein-protein interactions. The encoded protein is the E3 ubiquitin-protein ligase component of the linear ubiquitin chain assembly complex. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]
    Expression
    Ubiquitous expression in spleen (RPKM 17.0), testis (RPKM 12.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RNF31 in Genome Data Viewer
    Location:
    14q12
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (24146875..24160655)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (18345184..18358964)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (24616084..24629864)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5625 Neighboring gene ER membrane protein complex subunit 9 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5626 Neighboring gene microRNA 7703 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8190 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:24616442-24616942 Neighboring gene proteasome activator subunit 2 Neighboring gene RNA, 5S ribosomal pseudogene 383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8192 Neighboring gene interferon regulatory factor 9 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:24640701-24641201 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8193 Neighboring gene REC8 meiotic recombination protein Neighboring gene importin 4

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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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    Related articles in PubMed

    1. Effects of removing a highly conserved disulfide bond in ubiquitin-associated domain of human HOIP on biochemical characteristics. Ma W, et al. Protein Expr Purif, 2022 Feb. PMID 34695570
    2. Atypical ubiquitin ligase RNF31: the nuclear factor modulator in breast cancer progression. Zhu J, et al. BMC Cancer, 2016 Jul 26. PMID 27460922, Free PMC Article
    3. RNF31 represses cell progression and immune evasion via YAP/PD-L1 suppression in triple negative breast Cancer. Yang H, et al. J Exp Clin Cancer Res, 2022 Dec 29. PMID 36581998, Free PMC Article
    4. The E3 ligase HOIP specifies linear ubiquitin chain assembly through its RING-IBR-RING domain and the unique LDD extension. Smit JJ, et al. EMBO J, 2012 Oct 3. PMID 22863777, Free PMC Article
    5. Resonance assignments of the PUB domain of the RNF31 protein. Song L, et al. Biomol NMR Assign, 2023 Dec. PMID 37395936

    See all (193) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RNF31 promotes proliferation and invasion of hepatocellular carcinoma via nuclear factor kappaB activation.
      Title: RNF31 promotes proliferation and invasion of hepatocellular carcinoma via nuclear factor kappaB activation.
    2. Resonance assignments of the PUB domain of the RNF31 protein.
      Title: Resonance assignments of the PUB domain of the RNF31 protein.
    3. RNF31 promotes tumorigenesis via inhibiting RIPK1 kinase-dependent apoptosis.
      Title: RNF31 promotes tumorigenesis via inhibiting RIPK1 kinase-dependent apoptosis.
    4. RNF31 represses cell progression and immune evasion via YAP/PD-L1 suppression in triple negative breast Cancer.
      Title: RNF31 represses cell progression and immune evasion via YAP/PD-L1 suppression in triple negative breast Cancer.
    5. Effects of removing a highly conserved disulfide bond in ubiquitin-associated domain of human HOIP on biochemical characteristics.
      Title: Effects of removing a highly conserved disulfide bond in ubiquitin-associated domain of human HOIP on biochemical characteristics.
    6. RNF31 mediated ubiquitination of A20 aggravates inflammation and hepatocyte apoptosis through the TLR4/MyD88/NF-kappaB signaling pathway.
      Title: RNF31 mediated ubiquitination of A20 aggravates inflammation and hepatocyte apoptosis through the TLR4/MyD88/NF-κB signaling pathway.
    7. Site-specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling.
      Title: Site-specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling.
    8. Linear Ubiquitin Code: Its Writer, Erasers, Decoders, Inhibitors, and Implications in Disorders.
      Title: Linear Ubiquitin Code: Its Writer, Erasers, Decoders, Inhibitors, and Implications in Disorders.
    9. Cross-regulation between LUBAC and caspase-1 modulates cell death and inflammation.
      Title: Cross-regulation between LUBAC and caspase-1 modulates cell death and inflammation.
    10. Second Case of HOIP Deficiency Expands Clinical Features and Defines Inflammatory Transcriptome Regulated by LUBAC.
      Title: Second Case of HOIP Deficiency Expands Clinical Features and Defines Inflammatory Transcriptome Regulated by LUBAC.
    Submit: New GeneRIF Correction See all GeneRIFs (37)

    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

    Associated conditions

    Description Tests
    Immunodeficiency 115 with autoinflammation
    MedGen: C5882724 OMIM: 620632 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: IRF9

    Homology

    Clone Names

    • FLJ10111, FLJ23501, MGC19975

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables K48-linked polyubiquitin modification-dependent protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables K63-linked polyubiquitin modification-dependent protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables linear polyubiquitin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin binding IDA
    Inferred from Direct Assay
    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 ligase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in CD40 signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in T cell receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in defense response to bacterium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of necroptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of NF-kappaB transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of canonical NF-kappaB signal transduction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of protein targeting to mitochondrion HMP PubMed 
    involved_in positive regulation of xenophagy IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein linear polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein linear polyubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein polyubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of CD40 receptor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of LUBAC complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of LUBAC complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytoplasmic side of plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase RNF31
    Names
    HOIL-1-interacting protein
    RING-type E3 ubiquitin transferase RNF31
    zinc in-between-RING-finger ubiquitin-associated domain protein
    NP_001297261.1
    NP_060469.4

    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.

    Genomic

    1. NG_042234.1 RefSeqGene

      Range
      5624..18781
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1315

    mRNA and Protein(s)

    1. NM_001310332.2 → NP_001297261.1  E3 ubiquitin-protein ligase RNF31 isoform 2

      See identical proteins and their annotated locations for NP_001297261.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate first exon and an alternate splice site in a 5' exon compared to variant 1, resulting in the use of a downstream translation initiation site. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AL136295, AY256461, DA462121
      Consensus CDS
      CCDS81792.1
      UniProtKB/TrEMBL
      H0YNK5
      Related
      ENSP00000453574.1, ENST00000559275.5
      Conserved Domains (5) summary
      smart00647
      Location:628 → 690
      IBR; In Between Ring fingers
      cd14325
      Location:420 → 474
      UBA_RNF31; UBA domain found in E3 ubiquitin-protein ligase RING finger protein 31 and similar proteins
      sd00029
      Location:153 → 172
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam04981
      Location:548 → 598
      NMD3; NMD3 family
      pfam16678
      Location:332 → 476
      HOIP-UBA; UB-associated-like domain of HOIP or E3 ubiquitin-protein ligase

    2. NM_017999.5 → NP_060469.4  E3 ubiquitin-protein ligase RNF31 isoform 1

      See identical proteins and their annotated locations for NP_060469.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC012077, CN287790
      Consensus CDS
      CCDS41931.1
      UniProtKB/Swiss-Prot
      A0A962, Q86VI2, Q8TEI0, Q96EP0, Q96GB4, Q96NF1, Q9H5F1, Q9NWD2
      UniProtKB/TrEMBL
      A0A8V8TQD3
      Related
      ENSP00000315112.6, ENST00000324103.11
      Conserved Domains (6) summary
      cd10464
      Location:52 → 153
      PUB_RNF31; PNGase/UBA or UBX (PUB) domain of the RNF31 (or HOIP) protein
      smart00647
      Location:779 → 841
      IBR; In Between Ring fingers
      cd14325
      Location:571 → 625
      UBA_RNF31; UBA domain found in E3 ubiquitin-protein ligase RING finger protein 31 and similar proteins
      sd00029
      Location:304 → 323
      zf-RanBP2; RanBP2-type Zn finger [structural motif]
      pfam04981
      Location:699 → 749
      NMD3; NMD3 family
      pfam16678
      Location:483 → 627
      HOIP-UBA; UB-associated-like domain of HOIP or E3 ubiquitin-protein ligase

    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

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      24146875..24160655
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_018654722.1 Reference GRCh38.p14 PATCHES

      Range
      447853..461633
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      18345184..18358964
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96EP0.1 GenPept UniProtKB/Swiss-Prot:Q96EP0

    Gene LinkOut

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

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