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

Gene ID: 80352, updated on 5-Mar-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
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Genomic context

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Location:
6p22.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30070270..30075769, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (29934544..29940043, complement)
105.20220307 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: 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. 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. The HLA-B/-C haplotype block contains major determinants for host control of HIV. Trachtenberg E, et al. Genes Immun, 2009 Dec. PMID 19693088, Free PMC Article

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)

Genotypes

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 biological_process ND
No biological Data available
more info
  
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  
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_2023_10

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

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