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

RNF39 Gene

protein-coding   GIFtS: 48
GCID: GC06M030038

ring finger protein 39
 Explore 4 diseases affiliated with
RNF39 via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for RNF39    

Aliases
for RNF39 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Ring Finger Protein 391 2     HZF2 5
LIRF1 2 5     HZFw11
HZFW2 3 5     LTP (Long-Term Potentiation) Induced RING Finger Protein2
Protein HZFw2 3     

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


Summaries
for RNF39 gene

(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:
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)

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


Genomic Views
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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  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 plasmid: RNF39 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-,ALT_REF_LOCI_1 29,974,877-29,988,762      Chr6-,ALT_REF_LOCI_2 30,027,939-30,072,712      Chr6-,ALT_REF_LOCI_4 29,956,295-29,961,880     
Chr6-,ALT_REF_LOCI_6 30,027,629-30,068,786      Chr6-,ALT_REF_LOCI_3 30,028,370-30,044,993      Chr6-,ALT_REF_LOCI_5 30,031,364-30,036,949     

Proteins
for RNF39 gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H2S5

    • RNF39 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_079512.2  NP_739575.2  

    ENSEMBL proteins: 
     ENSP00000365942   ENSP00000244360  

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    Uscn 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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    Protein Domains /
    Families
    for RNF39 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    RNF39 for domains           About GeneDecksing

    5/8 InterPro domains/families (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 families:
    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


    Function
    for RNF39 gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section
    Function Summary:

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

    miRNA
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    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
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    Inhib. RNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008270zinc ion binding NAS--


    RNF39 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for RNF39:
     Decreased cilium length after  


    Pathways & Interactions
    for RNF39 gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 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



    Drugs & Compounds
    for RNF39 gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 

    Transcripts
    for RNF39 gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    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, 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 plasmid: RNF39 3' UTR sequence
    Inhib. RNA
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    Clone
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    Primer
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    Additional cDNA 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):

    AV656507 BF590977 NM_170769 BM875490 AI394569 NM_025236 BM916380 BM808118 
    AI732406 BG386787 BM711642 CA311242 BV183508 BM558545 AF238316 BX107891 
    AI733730 X90533 AA086121 BX379955 BF432584 BI018772 BM808012 BX388047 

    GeneLoc Exon Structure


    Expression
    for RNF39 gene

    (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)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ATTCCTACAT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image

    RNF39 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    CartilageLumbar Intervertebral DiscCartilage
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    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
    for RNF39 gene

    (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
    for RNF39 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    		  --

    Genomic Variants
    for RNF39 gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/143 NCBI SNPs in RNF39 are shown (see all 143)     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
    		--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
    rs1113011561,2
    		C,F,--30038942(+) CAGAAC/TAGCGG 4 L syn12Minor allele frequency- T:0.00NA EU 3503
    rs1469164571,2
    		F--30039005(+) AGTGAG/ACGGCC 3 /R int1 syn11Minor allele frequency- A:0.01NA 2466
    rs1390056141,2
    		C,F,--30039034(+) GCCCCG/CCTCCC 3 /R /G int1 mis11Minor allele frequency- C:0.01EU 219

    HapMap Linkage Disequilibrium report for RNF39 (30038043 - 30043664 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for RNF39: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RNF39
    DNA2.0 Custom Variant and Variant Library Synthesis for RNF39

    Disorders / Diseases
    for RNF39 gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    RNF39 for disorders           About GeneDecksing

    OMIM gene information: 607524    OMIM disorders: --

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

    Human Genome Epidemiology (HuGE) Navigator: RNF39 (6 documents)

    Export disorders for RNF39 gene to outside databases

    Publications
    for RNF39 gene

    (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 15):
    (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. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    3. 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)
    4. TRIM39 and RNF39 are associated with BehAset's disease independently of HLA-Ba8951 and -Aa8926. (PubMed id 20875797)1 Kurata R....Inoko H. (2010)
    5. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PubMed id 20593013)1 Cree B.A.... . (2010)
    6. Association of HLA-C and HCP5 gene regions with the clinical course of HIV-1 infection. (PubMed id 19050382)1 van Manen D....Schuitemaker H. (2009)
    7. 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 Barcellos L.F....Criswell L.A. (2009)
    8. The HLA-B/-C haplotype block contains major determina nts for host control of HIV. (PubMed id 19693088)1 Trachtenberg E....Wolinsky S. (2009)
    9. Common genetic variation and the control of HIV-1 in humans. (PubMed id 20041166)1 Fellay J....Goldstein D.B. (2009)
    10. Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). (PubMed id 19115949)1 Limou S....Zagury J.F. (2009)

    External Searches for RNF39 gene

    (in PubMed, OMIM, and NCBI Bookshelf)
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    Genome Databases showing RNF39 gene

    (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

    Other Databases showing RNF39 gene

    (According to HUGE)
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    Specialized Databases showing RNF39 gene

    (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

    Intellectual Property
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    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

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