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    RNF39 ring finger protein 39 [ Homo sapiens (human) ]

    Gene ID: 80352, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RNF39provided by HGNC
    Official Full Name
    ring finger protein 39provided by HGNC
    Primary source
    HGNC:HGNC:18064
    See related
    Ensembl:ENSG00000204618 MIM:607524; AllianceGenome:HGNC:18064
    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
    HZF; HZFW; LIRF; FAP216
    Summary
    This gene lies within the major histocompatibility complex class I region on chromosome 6. Studies of a similar rat protein suggest that this gene encodes a protein that plays a role in an early phase of synaptic plasticity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in small intestine (RPKM 5.5), duodenum (RPKM 5.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RNF39 in Genome Data Viewer
    Location:
    6p22.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30070270..30075769, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (29934544..29940043, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30038047..30043546, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene POLR1H antisense, pseudogene Neighboring gene eukaryotic translation termination factor 1 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30028069-30028935 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:30028936-30029801 Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 11 Neighboring gene RNA polymerase I subunit H Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:30041647-30042322 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:30042323-30042996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:30068196-30068705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:30070193-30070692 Neighboring gene TRIM31 antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:30080310-30081509 Neighboring gene tripartite motif containing 31 Neighboring gene small nucleolar RNA SNORA48

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Differential methylation at MHC in CD4(+) T cells is associated with multiple sclerosis independently of HLA-DRB1. Maltby VE, et al. Clin Epigenetics, 2017. PMID 28729889, Free PMC Article
    2. Combining omics data to identify genes associated with allergic rhinitis. Morin A, et al. Clin Epigenetics, 2017. PMID 28149331, Free PMC Article
    3. TRIM39 and RNF39 are associated with Behçet's disease independently of HLA-B∗51 and -A∗26. Kurata R, et al. Biochem Biophys Res Commun, 2010 Oct 29. PMID 20875797
    4. LIRF, a gene induced during hippocampal long-term potentiation as an immediate-early gene, encodes a novel RING finger protein. Matsuo R, et al. Biochem Biophys Res Commun, 2001 Nov 30. PMID 11716498
    5. Molecular cloning of testis-abundant finger Protein/Ring finger protein 23 (RNF23), a novel RING-B box-coiled coil-B30.2 protein on the class I region of the human MHC. Orimo A, et al. Biochem Biophys Res Commun, 2000 Sep 16. PMID 11006080

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The findings provide evidence that hypermethylation in an independent MHC locus, RNF39, is also associated with relapsing-remitting multiple sclerosis.
      Title: Differential methylation at MHC in CD4(+) T cells is associated with multiple sclerosis independently of HLA-DRB1.
    2. Results identified RNF39 as cis methylation quantitative trait loci in both allergic rhinitis and asthma.
      Title: Combining omics data to identify genes associated with allergic rhinitis.
    3. these findings suggest that RNF39 and TRIM39 are involved in the etiology of Behcet's disease.
      Title: TRIM39 and RNF39 are associated with Behçet's disease independently of HLA-B∗51 and -A∗26.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Common genetic variation and the control of HIV-1 in humans.
    EBI GWAS Catalog
    Genome-wide association study of proneness to anger.
    EBI GWAS Catalog
    Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02).
    EBI GWAS Catalog

    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

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    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
    		  
    Process Evidence Code Pubs
    involved_in innate immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RING finger protein 39
    Names
    LTP (long-term potentiation) induced RING finger protein
    protein HZFw

    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)

    1. NM_025236.4 → NP_079512.3  RING finger protein 39 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1), also known as HZFw1, represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL669914
      Consensus CDS
      CCDS4673.2
      UniProtKB/Swiss-Prot
      A2BEK3, A6NCD6, B0S858, Q5SPM8, Q5SPM9, Q5SPN0, Q5SRJ9, Q5SRK1, Q5SS29, Q9H2S3, Q9H2S4, Q9H2S5
      UniProtKB/TrEMBL
      Q96QB5
      Related
      ENSP00000244360.7, ENST00000244360.8
      Conserved Domains (4) summary
      TIGR00599
      Location:14 → 186
      rad18; DNA repair protein rad18
      cd12888
      Location:161 → 347
      SPRY_PRY_TRIM7_like; PRY/SPRY domain in tripartite motif-binding protein 7 (TRIM7)-like, including TRIM7, TRIM10, TRIM15, TRIM26, TRIM39, TRIM41
      cd00162
      Location:20 → 66
      RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]
      cl17238
      Location:18 → 66
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    2. NM_170769.3 → NP_739575.3  RING finger protein 39 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2), also known as HZFw2, lacks an in-frame segment in the coding region, compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
      Source sequence(s)
      AL669914
      Consensus CDS
      CCDS4674.2
      UniProtKB/TrEMBL
      A0A1U9X8G2
      Related
      ENSP00000365942.4, ENST00000376751.8
      Conserved Domains (4) summary
      TIGR00599
      Location:14 → 186
      rad18; DNA repair protein rad18
      cd00162
      Location:20 → 66
      RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]
      cl02614
      Location:161 → 257
      SPRY; SPRY domain
      cl17238
      Location:18 → 66
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      30070270..30075769 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017011325.2 → XP_016866814.1  RING finger protein 39 isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      1328362..1333861 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328523.1 → XP_054184498.1  RING finger protein 39 isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      1550041..1555540 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329914.1 → XP_054185889.1  RING finger protein 39 isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      1326186..1331685 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330406.1 → XP_054186381.1  RING finger protein 39 isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      1331020..1336519 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330685.1 → XP_054186660.1  RING finger protein 39 isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      1414360..1419859 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330899.1 → XP_054186874.1  RING finger protein 39 isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      1325430..1330924 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      1369189..1374688 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331419.1 → XP_054187394.1  RING finger protein 39 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      29934544..29940043 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356472.1 → XP_054212447.1  RING finger protein 39 isoform X1

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_170770.1: Suppressed sequence

      Description
      NM_170770.1: This RefSeq was permanently suppressed because currently there is not sufficient data to support this transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H2S5.2 GenPept UniProtKB/Swiss-Prot:Q9H2S5

    Gene LinkOut

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

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