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] See more...

Aliases for RNF39 Gene

Aliases for RNF39 Gene

  • Ring Finger Protein 39 2 3 5
  • RING Finger Protein 39 3 4
  • 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
  • GC06M030432
  • GC06M030482
  • GC06M030515
  • GC06M030098
  • GC06M030168
  • GC06M030217
  • GC06M030243
  • GC06M030277
  • GC06M030311
  • GC06M030354
  • GC06M030392

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 PML.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification 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
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J030074 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 506.2 +0.3 299 2.4 ZNF217 CTCF ZFX POLR2A TGIF2 ZBTB7A TEAD1 TBX3 ZKSCAN8 HDAC2 RNF39 ENSG00000237669 HLA-K ZFP57 ZNRD1 ZNRD1ASP HLA-A MICE HSALNG0049116
GH06J030077 Enhancer 0.2 Ensembl 500.7 -1.7 -1714 0.4 RNF39 HLA-K HLA-W IFITM4P piR-61580-542
GH06J030111 Promoter/Enhancer 1.1 Ensembl ENCODE 7 -36.8 -36766 2.9 SP1 NCOR1 EP300 RELA TEAD1 EZH2 FOXA2 CEBPB TBP NBN TRIM31 lnc-RNF39-5 HLA-U HLA-H ZFP57 ZNRD1ASP HCG4 RNF39 HCG18 HLA-A
GH06J030100 Promoter/Enhancer 1.6 FANTOM5 ENCODE CraniofacialAtlas 2.8 -26.2 -26193 3.9 FOXK2 ZNF217 CTCF NRF1 TCF12 POLR2G NCOR1 PHF8 ZNF639 ZNF10 TRIM31-AS1 HLA-K RPL23AP1 HCG4 MICD ZNRD1ASP ENSG00000237669 HLA-J ABCF1 HLA-W
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RNF39 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RNF39

Top Transcription factor binding sites by QIAGEN in the RNF39 gene promoter:
  • AP-4
  • Bach2
  • GATA-3
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4
  • RORalpha2
  • RREB-1

Genomic Locations for RNF39 Gene

Genomic Locations for RNF39 Gene
chr6:30,070,266-30,075,887
(GRCh38/hg38)
Size:
5,622 bases
Orientation:
Minus strand
chr6:30,038,043-30,043,664
(GRCh37/hg19)
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
    SequenceCaution:

    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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RNF39 Gene

Blocks:
  • Zn-finger, RING
  • Butyrophylin C-terminal DUF signature
  • SPRY-associated domain
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RNF39 Gene

GenScript: Design optimal peptide antigens:
  • Ring finger protein 39 (Q2L6J4_HUMAN)
  • Protein HZFw (RNF39_HUMAN)
genes like me logo Genes that share domains with RNF39: view

No data available for Graphical View of Domain Structure and 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

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RNF39

Clone 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

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
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (2)
  • Plasma membrane (2)
  • Vesicles (2)
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

PathCards logo

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

mRNA/cDNA for RNF39 Gene

3 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RNF39

Clone 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

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 and MOPED for RNF39 Gene



Protein tissue co-expression partners for RNF39 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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

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
chimpanzee
(Pan troglodytes)
Mammalia RNF39 31 30
  • 99.44 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RNF39 30
  • 87.33 (n)
dog
(Canis familiaris)
Mammalia RNF39 31 30
  • 85.19 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rnf39 17 31 30
  • 82.48 (n)
rat
(Rattus norvegicus)
Mammalia Rnf39 30
  • 81.63 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RNF39 31
  • 55 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 34 (a)
OneToMany
-- 31
  • 30 (a)
OneToMany
-- 31
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for RNF39: view image

Paralogs for RNF39 Gene

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

  • RNF39_HUMAN
  • Q2L6J4_HUMAN
genes like me logo Genes that share paralogs with RNF39: view

Variants for RNF39 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RNF39 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs1057539 - p.Asp268Asn
rs2074479 - p.Ser203Pro
rs2301752 - p.Ala245Thr
rs2301753 - p.Ala304Glu

Additional dbSNP identifiers (rs#s) for RNF39 Gene

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
RNF39

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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 54
  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 41 54
  3. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 41 54
  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 41 54
  5. Common genetic variation and the control of HIV-1 in humans. (PMID: 20041166) Fellay J … NIAID Center for HIV/AIDS Vaccine Immunology (CHAVI) (PLoS genetics 2009) 3 41 54

Products for RNF39 Gene

  • Signalway ELISA kits for RNF39
  • Signalway Proteins for RNF39

Sources for RNF39 Gene