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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

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. Diseases associated with RNF39 include Behcet Syndrome. An important paralog of this gene is MEFV.

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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06F030111 1.1 Ensembl ENCODE 7 -36.8 -36766 2.9 HDGF TBP PKNOX1 ATF1 CEBPG BMI1 EBF1 ZNF644 RARA RELA HLA-U HLA-H ZFP57 ZNRD1ASP HCG4 TRIM31 RNF39 HCG18 HLA-A HLA-L
GH06F030074 0.9 ENCODE 6.3 +0.0 45 1.9 ELF3 ARID4B ZNF48 RAD21 ZBTB40 ZNF2 RARA GLIS2 FOS THAP11 HCG4P3 HLA-K ZNRD1 ZNRD1ASP RNF39 PPP1R11
GH06F030100 1.7 FANTOM5 Ensembl ENCODE 2.8 -26.2 -26194 3.9 MLX WRNIP1 ARID4B DMAP1 SLC30A9 ZNF143 ZNF263 SP3 SP5 ZHX2 HLA-K RPL23AP1 TRIM31-AS1 HCG4 MICD ZNRD1ASP ETF1P1 PPP1R10 HCG18 PAIP1P1
GH06F030065 1.2 ENCODE 0.4 +9.1 9082 3.0 HDGF PKNOX1 ARNT CREB3L1 ZFP64 ARID4B SIN3A DMAP1 YBX1 ZNF2 HCG4P3 PPP1R10 IFITM4P HLA-A TRIM26 PAIP1P1 RPL7P4 HCG4P7 HLA-P UBQLN1P1
GH06F030094 1.2 Ensembl ENCODE 0.3 -19.5 -19532 1.6 ELF3 CBX3 MLX ARID4B THRB ZNF48 ZSCAN9 RARA FOS CREM HLA-U HLA-K HCG4 ZFP57 PPP1R11 HLA-W TRIM31-AS1 RNF39
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00000487593 487 801 ELF3 ARID4B BMI1 ZNF48 RAD21 ZBTB40 ZNF2 RARA GLIS2 THAP11

Genomic Location for RNF39 Gene

Chromosome:
6
Start:
30,070,266 bp from pter
End:
30,075,887 bp from pter
Size:
5,622 bases
Orientation:
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:
    Q9H2S5-RNF39_HUMAN
    Recommended name:
    RING finger protein 39
    Protein Accession:
    Q9H2S5
    Secondary Accessions:
    • A2BEK3
    • A6NCD6
    • B0S858
    • Q5SPM8
    • Q5SPM9
    • Q5SPN0
    • Q5SRJ9
    • Q5SRK1
    • Q5SS29
    • Q9H2S3
    • Q9H2S4

    Protein attributes for RNF39 Gene

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

    Alternative splice isoforms for RNF39 Gene

    UniProtKB/Swiss-Prot:

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

Suggested Antigen Peptide Sequences for RNF39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H2S5

UniProtKB/Swiss-Prot:

RNF39_HUMAN :
  • Contains 1 B30.2/SPRY domain.
  • Contains 1 RING-type zinc finger.
Domain:
  • Contains 1 B30.2/SPRY domain.
Similarity:
  • 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.

Gene Ontology (GO) - Molecular Function for RNF39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008270 zinc ion binding IEA --
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

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , 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

Cytoplasm.

Subcellular locations from

COMPARTMENTS
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

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

Transcripts for RNF39 Gene

Unigene Clusters for RNF39 Gene

Ring finger protein 39:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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

No ASD Table

Relevant External Links for RNF39 Gene

GeneLoc Exon Structure for
RNF39
ECgene alternative splicing isoforms for
RNF39

Expression for RNF39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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:

RNF39

SOURCE GeneReport for Unigene cluster for RNF39 Gene:

Hs.121178

mRNA Expression by UniProt/SwissProt for RNF39 Gene:

Q9H2S5-RNF39_HUMAN
Tissue specificity: Expressed in testis.
genes like me logo Genes that share expression patterns with RNF39: view

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
chimpanzee
(Pan troglodytes)
Mammalia RNF39 34 35
  • 99.44 (n)
cow
(Bos Taurus)
Mammalia RNF39 34
  • 87.33 (n)
dog
(Canis familiaris)
Mammalia RNF39 34 35
  • 85.19 (n)
mouse
(Mus musculus)
Mammalia Rnf39 34 16 35
  • 82.48 (n)
rat
(Rattus norvegicus)
Mammalia Rnf39 34
  • 81.63 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RNF39 35
  • 55 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 34 (a)
OneToMany
-- 35
  • 30 (a)
OneToMany
-- 35
  • 21 (a)
OneToMany
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

ENSEMBL:
Gene Tree for RNF39 (if available)
TreeFam:
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
rs1051133 -- 30,070,131(+) CTCTT(A/T)CCTCT downstream-variant-500B, utr-variant-3-prime
rs1057539 -- 30,071,572(-) GCTTC(A/G)ATCAG downstream-variant-500B, reference, missense
rs10947050 -- 30,072,514(+) AGTGA(C/T)GAGAG intron-variant
rs10947051 -- 30,078,228(+) TTCTC(A/G)TTCCC utr-variant-5-prime
rs10947052 -- 30,078,234(+) TTCCC(C/T)GAGCC utr-variant-5-prime

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)

Relevant External Links for RNF39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNF39

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

Disorders for RNF39 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RNF39 Gene - From: DISEASES

Disorder Aliases PubMed IDs
behcet syndrome
  • behcet's disease
- elite association - COSMIC cancer census association via MalaCards
Search RNF39 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RNF39

Genetic Association Database (GAD)
RNF39
Human Genome Epidemiology (HuGE) Navigator
RNF39
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RNF39
genes like me logo Genes that share disorders with RNF39: view

No data available for 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 64
  2. 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 46 64
  3. Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). (PMID: 19115949) Limou S. … Zagury J.F. (J. Infect. Dis. 2009) 3 46 64
  4. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos L.F. … Criswell L.A. (PLoS Genet. 2009) 3 46 64
  5. Common genetic variation and the control of HIV-1 in humans. (PMID: 20041166) Fellay J. … Goldstein D.B. (PLoS Genet. 2009) 3 46 64

Products for RNF39 Gene

Sources for RNF39 Gene

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