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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RNF39 Gene

protein-coding   GIFtS: 49
GCID: GC06M030038

Ring Finger Protein 39

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Ring Finger Protein 391 2
HZFW2 3 5
Protein HZFw2 3
HZF2 5
LIRF2 5
LTP (Long-Term Potentiation) Induced RING Finger Protein2

External Ids:    HGNC: 180641   Entrez Gene: 803522   Ensembl: ENSG000002046187   OMIM: 6075245   UniProtKB: Q9H2S53   

Export aliases for RNF39 gene to outside databases

Previous GC identifers: GC06M029808 GC06M030144 GC06M030146 GC06M029837


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for RNF39 Gene:
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)

GeneCards Summary for RNF39 Gene: 
RNF39 (ring finger protein 39) is a protein-coding gene. Diseases associated with RNF39 include behcet's disease, and systemic lupus erythematosus. GO annotations related to this gene include zinc ion binding. An important paralog of this gene is RFPL1.

UniProtKB/Swiss-Prot: RNF39_HUMAN, Q9H2S5
Function: May play a role in prolonged long term-potentiation (LTP) maintenance (By similarity)

Gene Wiki entry for RNF39 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.2  NT_007592.15  NT_113891.2  NT_167244.1  NT_167245.1  NT_167246.1  NT_167247.1  
NT_167248.1  NT_167249.1  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RNF39 gene promoter:
         NF-AT4   NF-AT2   GATA-3   RREB-1   Bach2   NF-AT3   AP-4   NF-AT1   NF-AT   RORalpha2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRNF39 promoter sequence
   Search SABiosciences Chromatin IP Primers for RNF39

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RNF39


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p21.3   Ensembl cytogenetic band:  6p22.1   HGNC cytogenetic band: 6p21.3

RNF39 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNF39 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M030038:  view genomic region     (about GC identifiers)

Start:
30,038,043 bp from pter      End:
30,043,664 bp from pter
Size:
5,622 bases      Orientation:
minus strand

6/7 alternative locations (see all 7):
Chr6-,NT_167245 1,331,767-1,337,352      Chr6-,NT_167249 1,368,483-1,374,068      Chr6-,NT_167247 1,419,941-1,425,526     
Chr6-,NT_167246 1,336,636-1,342,221      Chr6-,NT_113891.2 1,550,143-1,555,728      Chr6-,NT_167244 1,278,274-1,283,859     

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RNF39_HUMAN, Q9H2S5 (See protein sequence)
Recommended Name: RING finger protein 39  
Size: 420 amino acids; 45525 Da
Subcellular location: Cytoplasm (By similarity)
Secondary accessions: A2BEK3 A6NCD6 B0S858 Q5SPM8 Q5SPM9 Q5SPN0 Q5SRJ9 Q5SRK1 Q5SS29 Q9H2S3
Q9H2S4
Alternative splicing: 3 isoforms:  Q9H2S5-1   Q9H2S5-2   Q9H2S5-3   (Ref.1 (AAG40630) sequence differs from that show due to a frameshift in position 237)

Explore the universe of human proteins at neXtProt for RNF39: NX_Q9H2S5

Explore proteomics data for RNF39 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9H2S5

  • RNF39 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RNF39 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_079512.2  NP_739575.2  

    ENSEMBL proteins: 
     ENSP00000365942   ENSP00000244360  

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    Cloud-Clone Corp. Proteins for RNF39 

    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005737cytoplasm IEA--

    RNF39 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    RNF: RING-type (C3HC4) zinc fingers

    5/8 InterPro protein domains (see all 8):
     IPR006574 PRY
     IPR017907 Znf_RING_CS
     IPR001841 Znf_RING
     IPR001870 B30.2/SPRY
     IPR003877 SPRY_rcpt

    Graphical View of Domain Structure for InterPro Entry Q9H2S5

    ProtoNet protein and cluster: Q9H2S5

    3 Blocks protein domains:
    IPB001841 Zn-finger
    IPB003879 Butyrophylin C-terminal DUF signature
    IPB006574 SPRY-associated domain


    UniProtKB/Swiss-Prot: RNF39_HUMAN, Q9H2S5
    Similarity: Contains 1 B30.2/SPRY domain
    Similarity: Contains 1 RING-type zinc finger


    RNF39 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RNF39_HUMAN, Q9H2S5
    Function: May play a role in prolonged long term-potentiation (LTP) maintenance (By similarity)

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding ----
    GO:0008270zinc ion binding NAS--
    GO:0046872metal ion binding ----
         
    RNF39 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for RNF39:
     Decreased cilium length after  

    Animal Models:
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    SwitchGear 3'UTR luciferase reporter plasmidRNF39 3' UTR sequence
    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RNF39

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for RNF39 (ENSP000002443604) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PPP1CBENSP000002961224STRING: ENSP00000296122
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008150biological_process ND--

    RNF39 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for RNF39

    Search CenterWatch for drugs/clinical trials and news about RNF39

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for RNF39 gene (3 alternative transcripts): 
    NM_170770.1  NM_025236.3  NM_170769.2  

    Unigene Cluster for RNF39:

    Ring finger protein 39
    Hs.121178  [show with all ESTs]
    Unigene Representative Sequence: NM_025236
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000376751 ENST00000244360(uc003npd.3 uc003npe.3)
    miRNA
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    8 QIAGEN miScript miRNA Assays for microRNAs that regulate RNF39:
    hsa-miR-1273d hsa-miR-3152-3p hsa-miR-137 hsa-miR-29c hsa-miR-29a hsa-miR-767-5p hsa-miR-181a-2* hsa-miR-29b
    SwitchGear 3'UTR luciferase reporter plasmidRNF39 3' UTR sequence
    Inhib. RNA
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    Additional mRNA sequence: 

    AF238315.1 AF238316.1 AF238317.1 

    9 DOTS entries:

    DT.421508  DT.446865  DT.121346035  DT.100879013  DT.65286602  DT.100879022  DT.121346122  DT.75189370 
    DT.95165665 

    24/63 AceView cDNA sequences (see all 63):

    NM_025236 AI394569 AV656507 NM_170769 BM875490 BF590977 BX394689 BU179181 
    BX388047 BX107891 CA311242 X90533 BI018772 BM916380 BM808012 BM711642 
    AA086121 AF238316 AF238315 BV183508 BG386787 AI784065 AI732406 BM808118 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RNF39 expression in normal human tissues (normalized intensities)      RNF39 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ATTCCTACAT
    RNF39 Expression
    About this image


    RNF39 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/4 selected tissues (see all 4) fully expand
     
     Blood (Hematopoietic System)
             Hematopoietic Stem Cells Hematopoietic Bone Marrow
     
     Oral Cavity (Gastrointestinal Tract)
             buccal mucosa   
     
     Thyroid (Endocrine System)
     
     Larynx (Respiratory System)

    See RNF39 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RNF39

    SOURCE GeneReport for Unigene cluster: Hs.121178

    UniProtKB/Swiss-Prot: RNF39_HUMAN, Q9H2S5
    Tissue specificity: Expressed in testis

        SABiosciences Custom PCR Arrays for RNF39
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of human and mouse.

    Orthologs for RNF39 gene from 1/6 species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rnf391 , 5 ring finger protein 391, 5 82.48(n)1
    83.24(a)1
      17 (19.16 cM)5
    3864541  NM_001099632.11  NP_001093102.11 
     369429185 


    ENSEMBL Gene Tree for RNF39 (if available)
    TreeFam Gene Tree for RNF39 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RNF39 gene
    RFPL12  MEFV2  RFPL4AL12  RFPL32  RFPL4A2  RFPL22  RFPL4B2  
    2 SIMAP similar genes for RNF39 using alignment to 4 protein entries:     RNF39_HUMAN (see all proteins):
    HCGV    TRIM39

    RNF39 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/196 SNPs in RNF39 are shown (see all 196)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs92612901,2
    C,F,H--30038647(+) TGTAGT/CAGCTG 2 -- ut31 ese324Minor allele frequency- C:0.05NS EA NA EU 3054
    rs1397526071,2
    C--30038708(+) GAGCAA/GGGACG 2 -- ut310--------
    rs92612911,2
    C,F,H--30038712(+) AGGGAC/TGTGGA 2 -- ut31 ese312Minor allele frequency- T:0.20NS EA WA CSA NA EU 1288
    rs1176149981,2
    C,F--30038720(+) GGAAAC/TGTGGA 2 -- ut312Minor allele frequency- T:0.01EA EU 653
    rs1864375491,2
    --30038731(+) GACCAC/GGTGAG 2 -- ut310--------
    rs737281071,2
    C,F--30038823(+) GGGGAA/GTTCCA 2 -- ut316Minor allele frequency- G:0.12WA NA EA EU 925
    rs92612921,2
    C,F--30038830(+) TCCACC/GCCCAA 2 -- ut316Minor allele frequency- G:0.18WA CSA NA EA EU 895
    rs3728823861,2
    C--30038875(+) TCTAGC/TTGGAG 2 -- ut310--------
    rs1113011561,2
    C,F--30038942(+) CAGAAC/TAGCGG 4 L syn12Minor allele frequency- T:0.00NA EU 3503
    rs1469164571,2
    C,F--30039005(+) AGTGAG/ACGGCC 3 /R int1 syn11Minor allele frequency- A:0.01NA 2466

    HapMap Linkage Disequilibrium report for RNF39 (30038043 - 30043664 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for RNF39:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2731777CNV Deletion23290073
    nsv884049CNV Loss21882294

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 607524    OMIM disorders: --

    4 diseases for RNF39:    About MalaCards
    behcet's disease    systemic lupus erythematosus    multiple sclerosis    lupus erythematosus


    RNF39 for disorders           About GeneDecksing

    Genetic Association Database (GAD): RNF39
    Human Genome Epidemiology (HuGE) Navigator: RNF39 (6 documents)

    Export disorders for RNF39 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for RNF39 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with RNF39)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Transcriptional analysis of the 69-kb sequence centromeric to HLA-J: a dense and complex structure of five genes. (PubMed id 11130983)1, 2, 3 Coriton O.... Mosser J. (2000)
    2. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PubMed id 20593013)1, 4 Cree B.A.... . (2010)
    3. Common genetic variation and the control of HIV-1 in humans. (PubMed id 20041166)1, 4 Fellay J....Goldstein D.B. (2009)
    4. Association of HLA-C and HCP5 gene regions with the clinical course of HIV-1 infection. (PubMed id 19050382)1, 4 van Manen D....Schuitemaker H. (2009)
    5. High-density SNP screening of the major histocompatib ility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1, 4 Barcellos L.F....Criswell L.A. (2009)
    6. The HLA-B/-C haplotype block contains major determina nts for host control of HIV. (PubMed id 19693088)1, 4 Trachtenberg E....Wolinsky S. (2009)
    7. Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). (PubMed id 19115949)1, 4 Limou S....Zagury J.F. (2009)
    8. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    9. LIRF, a gene induced during hippocampal long-term pot entiation as an immediate-early gene, encodes a novel RING finger protein. (PubMed id 11716498)1, 3 Matsuo R....Inokuchi K. (2001)
    10. Genome-wide association study identifies variants in the MHC class I, IL10, and IL23R-IL12RB2 regions associated with BehAset's disea se. (PubMed id 20622878)4 Remmers E.F....GA1l A. (2010)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 80352 HGNC: 18064 AceView: RNF39 Ensembl:ENSG00000204618 euGenes: HUgn80352
    ECgene: RNF39 H-InvDB: RNF39

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RNF39 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RNF39 gene:
    Search GeneIP for patents involving RNF39

    GeneCards and IP:
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