Free for academic non-profit institutions. Other users need a Commercial license

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

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 RFPL4A.

UniProtKB/Swiss-Prot for RNF39 Gene

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

Gene Wiki entry for RNF39 Gene

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

Genomics for RNF39 Gene

Regulatory Elements for RNF39 Gene

Enhancers for RNF39 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around RNF39 on UCSC Golden Path with GeneCards custom track

Promoters for RNF39 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around RNF39 on UCSC Golden Path with GeneCards custom track

Genomic Location for RNF39 Gene

30,070,266 bp from pter
30,075,887 bp from pter
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

Proteomics data for RNF39 Gene at MOPED

Post-translational modifications for RNF39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RNF39 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RNF39 Gene

Domains & Families for RNF39 Gene

Gene Families for RNF39 Gene

Suggested Antigen Peptide Sequences for RNF39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 B30.2/SPRY domain.
  • Contains 1 RING-type zinc finger.
  • Contains 1 B30.2/SPRY domain.
  • Contains 1 RING-type zinc finger.
genes like me logo Genes that share domains with RNF39: view

Function for RNF39 Gene

Molecular function for RNF39 Gene

UniProtKB/Swiss-Prot Function:
May play a role in prolonged long term-potentiation (LTP) maintenance.
genes like me logo Genes that share phenotypes with RNF39: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , 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

Jensen Localization Image for RNF39 Gene COMPARTMENTS Subcellular localization image for RNF39 gene
Compartment Confidence
nucleus 3
cytosol 2
mitochondrion 1

No data available for Gene Ontology (GO) - Cellular Components for RNF39 Gene

Pathways & Interactions for RNF39 Gene

SuperPathways for RNF39 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RNF39 Gene


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

mRNA/cDNA for RNF39 Gene

Unigene Clusters for RNF39 Gene

Ring finger protein 39:
Representative Sequences:

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 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

SOURCE GeneReport for Unigene cluster for RNF39 Gene Hs.121178

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

Protein tissue co-expression partners for RNF39 Gene

Primer Products

Orthologs for RNF39 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RNF39 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia RNF39 35
  • 87.33 (n)
  • 85.43 (a)
(Canis familiaris)
Mammalia RNF39 35
  • 85.19 (n)
  • 86.61 (a)
RNF39 36
  • 85 (a)
(Mus musculus)
Mammalia Rnf39 35
  • 82.48 (n)
  • 83.24 (a)
Rnf39 16
Rnf39 36
  • 83 (a)
(Pan troglodytes)
Mammalia RNF39 35
  • 99.44 (n)
  • 99.29 (a)
RNF39 36
  • 99 (a)
(Rattus norvegicus)
Mammalia Rnf39 35
  • 81.63 (n)
  • 81.82 (a)
(Ornithorhynchus anatinus)
Mammalia RNF39 36
  • 55 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 30 (a)
-- 36
  • 21 (a)
-- 36
  • 34 (a)
Species with no ortholog for RNF39:
  • 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 Sequence Context AA Info Type
rs2074479 - 30,073,232(-) CAACA(C/T)CCAAG reference, missense
rs2301752 - 30,071,641(-) TCTCC(A/G)CCGAC reference, missense
rs1057539 - 30,071,572(-) GCTTC(A/G)ATCAG reference, missense
rs2301753 - 30,071,463(-) GGATG(A/C)GGACG reference, missense
rs1150735 -- 30,077,422(-) caggc(C/T)gatca upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
esv2731777 CNV Deletion 23290073
nsv884049 CNV Loss 21882294

Variation tolerance for RNF39 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for RNF39 Gene

Disorders for RNF39 Gene

Relevant External Links for RNF39

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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. (Mamm. Genome 2000) 2 3 4 67
  2. LIRF, a gene induced during hippocampal long-term potentiation as an immediate-early gene, encodes a novel RING finger protein. (PMID: 11716498) Matsuo R. … Inokuchi K. (Biochem. Biophys. Res. Commun. 2001) 2 3
  3. Genome-wide association study of proneness to anger. (PMID: 24489884) Mick E. … Goldberg R.J. (PLoS ONE 2014) 3
  4. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PMID: 20593013) Cree B.A. … . (PLoS ONE 2010) 3
  5. TRIM39 and RNF39 are associated with BehAset's disease independently of HLA-Ba8951 and -Aa8926. (PMID: 20875797) Kurata R. … Inoko H. (Biochem. Biophys. Res. Commun. 2010) 3

Products for RNF39 Gene

Sources for RNF39 Gene