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Aliases for RNF39 Gene

Aliases for RNF39 Gene

  • Ring Finger Protein 39 2 3 5
  • Protein HZFw 3 4
  • HZFW 3 4
  • LTP (Long-Term Potentiation) Induced RING Finger Protein 3
  • LIRF 3
  • HZF 3

External Ids for RNF39 Gene

Previous GeneCards Identifiers for RNF39 Gene

  • GC06M029808
  • GC06M030144
  • GC06M030146
  • GC06M030038
  • GC06M029837
  • GC06M030084
  • GC06M030085
  • GC06M030098
  • GC06M030168
  • GC06M030217
  • GC06M030243
  • GC06M030277

Summaries for RNF39 Gene

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. An important paralog of this gene is RFPL2.

UniProtKB/Swiss-Prot for RNF39 Gene

  • May play a role in prolonged long term-potentiation (LTP) maintenance.

Gene Wiki entry for RNF39 Gene

Additional gene information for RNF39 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RNF39 Gene

Genomics for RNF39 Gene

GeneHancer (GH) Regulatory Elements for RNF39 Gene

Promoters and enhancers for RNF39 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I030074 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 556.3 +0.4 402 2.6 ELF3 FOXA2 ARID4B SIN3A ZNF2 RAD21 ZNF48 RARA GLIS2 ZNF143 RNF39 HCG4P3 HLA-K ZFP57 ZNRD1 ZNRD1ASP HLA-A MICE PPP1R11
GH06I030111 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 7 -36.8 -36766 2.9 HDGF PKNOX1 FOXA2 BMI1 BATF RARA ATF7 IKZF2 RXRA CEBPB TRIM31 HLA-U HLA-H ZFP57 ZNRD1ASP HCG4 RNF39 HCG18 HLA-A HLA-L
GH06I030100 Enhancer 1.5 FANTOM5 Ensembl ENCODE 2.8 -26.2 -26193 3.9 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 SLC30A9 ZNF143 SP3 SP5 HLA-K RPL23AP1 TRIM31-AS1 HCG4 MICD ZNRD1ASP HCG4P3 HLA-J ABCF1 HLA-W
GH06I030065 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 0.4 +9.1 9082 3 ZFP64 DMAP1 YBX1 YY1 SLC30A9 E2F8 ZNF143 ZNF263 SP3 NFYC PPP1R11 HCG4P3 TRIM26 TRIM39 MDC1 PPP1R10 ZNRD1 HLA-A ETF1P1 PAIP1P1
GH06I030090 Enhancer 1 Ensembl ENCODE 0.4 -15.9 -15886 2 ELF3 PKNOX1 MLX SIN3A ZNF48 RARA SLC30A9 RCOR1 FOS SMARCC1 HCG4P3 HLA-K HCG4 ZNRD1 HLA-A HLA-W TRIM31-AS1 RNF39
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RNF39 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RNF39 gene promoter:

Genomic Locations for RNF39 Gene

Genomic Locations for RNF39 Gene
5,622 bases
Minus strand

Genomic View for RNF39 Gene

Genes around RNF39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNF39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNF39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for RNF39 Gene

  • Protein details for RNF39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    RING finger protein 39
    Protein Accession:
    Secondary Accessions:
    • A2BEK3
    • A6NCD6
    • B0S858
    • Q5SPM8
    • Q5SPM9
    • Q5SPN0
    • Q5SRJ9
    • Q5SRK1
    • Q5SS29
    • Q9H2S3
    • Q9H2S4

    Protein attributes for RNF39 Gene

    420 amino acids
    Molecular mass:
    45525 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for RNF39 Gene


neXtProt entry for RNF39 Gene

Post-translational modifications for RNF39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RNF39 Gene

No data available for DME Specific Peptides for RNF39 Gene

Domains & Families for RNF39 Gene

Gene Families for RNF39 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for RNF39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RNF39: view

No data available for UniProtKB/Swiss-Prot for RNF39 Gene

Function for RNF39 Gene

Molecular function for RNF39 Gene

UniProtKB/Swiss-Prot Function:
May play a role in prolonged long term-potentiation (LTP) maintenance.

Phenotypes From GWAS Catalog for RNF39 Gene

Gene Ontology (GO) - Molecular Function for RNF39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RNF39: view
genes like me logo Genes that share phenotypes with RNF39: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RNF39 Gene

Localization for RNF39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNF39 Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RNF39 gene
Compartment Confidence
nucleus 3
cytosol 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (1)
  • Plasma membrane (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RNF39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005575 cellular_component ND --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with RNF39: view

Pathways & Interactions for RNF39 Gene

SuperPathways for RNF39 Gene

No Data Available

Interacting Proteins for RNF39 Gene

Gene Ontology (GO) - Biological Process for RNF39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with RNF39: view

No data available for Pathways by source and SIGNOR curated interactions for RNF39 Gene

Drugs & Compounds for RNF39 Gene

No Compound Related Data Available

Transcripts for RNF39 Gene

Unigene Clusters for RNF39 Gene

Ring finger protein 39:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RNF39 Gene

No ASD Table

Relevant External Links for RNF39 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RNF39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNF39 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RNF39 Gene

This gene is overexpressed in Skin - Not Sun Exposed (Suprapubic) (x11.7), Skin - Sun Exposed (Lower leg) (x10.9), Esophagus - Mucosa (x5.7), Minor Salivary Gland (x5.2), and Vagina (x4.1).

Protein differential expression in normal tissues from HIPED for RNF39 Gene

This gene is overexpressed in Frontal cortex (34.7) and Cervix (20.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RNF39 Gene

Protein tissue co-expression partners for RNF39 Gene

NURSA nuclear receptor signaling pathways regulating expression of RNF39 Gene:


SOURCE GeneReport for Unigene cluster for RNF39 Gene:


mRNA Expression by UniProt/SwissProt for RNF39 Gene:

Tissue specificity: Expressed in testis.
genes like me logo Genes that share expression patterns with RNF39: view

Primer Products

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNF39 Gene

Orthologs for RNF39 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RNF39 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RNF39 33 34
  • 99.44 (n)
(Bos Taurus)
Mammalia RNF39 33
  • 87.33 (n)
(Canis familiaris)
Mammalia RNF39 33 34
  • 85.19 (n)
(Mus musculus)
Mammalia Rnf39 33 16 34
  • 82.48 (n)
(Rattus norvegicus)
Mammalia Rnf39 33
  • 81.63 (n)
(Ornithorhynchus anatinus)
Mammalia RNF39 34
  • 55 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 34 (a)
-- 34
  • 30 (a)
-- 34
  • 21 (a)
Species where no ortholog for RNF39 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for RNF39 Gene

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

Paralogs for RNF39 Gene

Paralogs for RNF39 Gene

(2) SIMAP similar genes for RNF39 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with RNF39: view

Variants for RNF39 Gene

Sequence variations from dbSNP and Humsavar for RNF39 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000209541 -- 30,074,167(-) C/G intron_variant
rs1000302971 -- 30,074,377(-) G/A intron_variant
rs1000417246 -- 30,071,585(-) G/A coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, synonymous_variant
rs1000485047 -- 30,080,250(-) G/T 5_prime_UTR_variant, genic_upstream_transcript_variant
rs1000535293 -- 30,079,041(-) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RNF39 Gene

Variant ID Type Subtype PubMed ID
esv2731777 CNV deletion 23290073
esv3411275 CNV duplication 20981092
nsv1074389 CNV deletion 25765185
nsv1122126 CNV deletion 24896259
nsv1144137 CNV deletion 24896259
nsv601264 CNV loss 21841781

Variation tolerance for RNF39 Gene

Gene Damage Index Score: 12.20; 93.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RNF39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNF39 Gene

Disorders for RNF39 Gene

Additional Disease Information for RNF39

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RNF39 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RNF39 Gene

Publications for RNF39 Gene

  1. Transcriptional analysis of the 69-kb sequence centromeric to HLA-J: a dense and complex structure of five genes. (PMID: 11130983) Coriton O … Mosser J (Mammalian genome : official journal of the International Mammalian Genome Society 2000) 2 3 4 58
  2. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PMID: 20593013) Cree BA … IMSGC (PloS one 2010) 3 44 58
  3. Association of HLA-C and HCP5 gene regions with the clinical course of HIV-1 infection. (PMID: 19050382) van Manen D … Schuitemaker H (AIDS (London, England) 2009) 3 44 58
  4. Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). (PMID: 19115949) Limou S … ANRS Genomic Group (The Journal of infectious diseases 2009) 3 44 58
  5. The HLA-B/-C haplotype block contains major determinants for host control of HIV. (PMID: 19693088) Trachtenberg E … Wolinsky S (Genes and immunity 2009) 3 44 58

Products for RNF39 Gene

Sources for RNF39 Gene

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