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Aliases for RNF38 Gene

Aliases for RNF38 Gene

  • Ring Finger Protein 38 2 3
  • RING Finger Protein 38 4 5
  • RING-Type E3 Ubiquitin Transferase RNF38 4
  • EC 2.3.2.27 4

External Ids for RNF38 Gene

Previous GeneCards Identifiers for RNF38 Gene

  • GC09M036648
  • GC09M036505
  • GC09M036326
  • GC09M036289

Summaries for RNF38 Gene

Entrez Gene Summary for RNF38 Gene

  • This gene encodes a protein with a coiled-coil motif and a RING-H2 motif (C3H2C2) at its carboxy-terminus. The RING motif is a zinc-binding domain found in a large set of proteins playing roles in diverse cellular processes including oncogenesis, development, signal transduction, and apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

GeneCards Summary for RNF38 Gene

RNF38 (Ring Finger Protein 38) is a Protein Coding gene. GO annotations related to this gene include ligase activity and ubiquitin-protein transferase activity. An important paralog of this gene is RNF44.

UniProtKB/Swiss-Prot for RNF38 Gene

  • Acts as an E3 ubiquitin-protein ligase able to ubiquitinate p53/TP53 which promotes its relocalization to discrete foci associated with PML nuclear bodies. Exhibits preference for UBE2D2 as a E2 enzyme.

Gene Wiki entry for RNF38 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RNF38 Gene

Genomics for RNF38 Gene

Regulatory Elements for RNF38 Gene

Enhancers for RNF38 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
GH09G036398 1.3 Ensembl ENCODE 19 +87.0 87048 4.7 HDGF FOXA2 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 ZNF207 RNF38 OR13E1P HRCT1 GLIPR2 HMGB3P24 MRPS21P4
GH09G036419 1 ENCODE 19 +67.6 67574 1.6 FOXA2 ZFP64 ARID4B ZNF48 YY1 FOS ZNF263 SP5 KAT8 NFIL3 RNF38 MELK GNE MRPS21P4
GH09G036406 1 Ensembl ENCODE 13.8 +80.3 80316 1.1 GTF2F1 ELF3 SOX13 HDGF CTCF SAP130 RAD21 ZNF143 ZNF207 SMC3 RNF38 MRPS21P4 HMGB3P24
GH09G036456 1.1 Ensembl ENCODE 12.5 +29.6 29569 3.0 FOXA2 BMI1 ZBTB40 ZNF207 FOS RELB ETV6 IKZF2 CREM CBFB RNF38 CLTA GNE MRPS21P4
GH09G036316 1.1 Ensembl ENCODE 4.4 +168.6 168593 4.6 NFIB MLX SIN3A DMAP1 RAD21 YY1 RARA GATA2 RCOR1 ZNF263 GLIPR2 GNE HMGB3P24 RNF38 MRPS21P4
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RNF38 on UCSC Golden Path with GeneCards custom track

Promoters for RNF38 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000234786 448 2601 HDGF FOXA2 ARNT CREB3L1 SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207

Genomic Location for RNF38 Gene

Chromosome:
9
Start:
36,336,396 bp from pter
End:
36,487,548 bp from pter
Size:
151,153 bases
Orientation:
Minus strand

Genomic View for RNF38 Gene

Genes around RNF38 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNF38 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNF38 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNF38 Gene

Proteins for RNF38 Gene

  • Protein details for RNF38 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H0F5-RNF38_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase RNF38
    Protein Accession:
    Q9H0F5
    Secondary Accessions:
    • A6PVP9
    • B1AM81
    • B1AM82
    • B3KSG4
    • E7EVL3
    • Q7LB33
    • Q8N0Y0
    • Q9H748

    Protein attributes for RNF38 Gene

    Size:
    515 amino acids
    Molecular mass:
    57595 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for RNF38 Gene

    Alternative splice isoforms for RNF38 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RNF38 Gene

Post-translational modifications for RNF38 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RNF38 Gene

Domains & Families for RNF38 Gene

Gene Families for RNF38 Gene

Protein Domains for RNF38 Gene

Suggested Antigen Peptide Sequences for RNF38 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RNF38: view

No data available for UniProtKB/Swiss-Prot for RNF38 Gene

Function for RNF38 Gene

Molecular function for RNF38 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.
UniProtKB/Swiss-Prot Function:
Acts as an E3 ubiquitin-protein ligase able to ubiquitinate p53/TP53 which promotes its relocalization to discrete foci associated with PML nuclear bodies. Exhibits preference for UBE2D2 as a E2 enzyme.

Enzyme Numbers (IUBMB) for RNF38 Gene

Gene Ontology (GO) - Molecular Function for RNF38 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IDA 23973461
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0061630 ubiquitin protein ligase activity IBA --
genes like me logo Genes that share ontologies with RNF38: view
genes like me logo Genes that share phenotypes with RNF38: view

Animal Models for RNF38 Gene

MGI Knock Outs for RNF38:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RNF38 Gene

Localization for RNF38 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNF38 Gene

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 RNF38 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for RNF38 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 23973461
GO:0005654 nucleoplasm IDA --
GO:0036126 sperm flagellum IEA --
genes like me logo Genes that share ontologies with RNF38: view

Pathways & Interactions for RNF38 Gene

SuperPathways for RNF38 Gene

No Data Available

UniProtKB/Swiss-Prot Q9H0F5-RNF38_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for RNF38 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008584 male gonad development IEA --
GO:0016567 protein ubiquitination IDA,IEA --
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process IBA --
genes like me logo Genes that share ontologies with RNF38: view

No data available for Pathways by source and SIGNOR curated interactions for RNF38 Gene

Drugs & Compounds for RNF38 Gene

No Compound Related Data Available

Transcripts for RNF38 Gene

Unigene Clusters for RNF38 Gene

Ring finger protein 38:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RNF38 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c ^ 11a · 11b · 11c · 11d · 11e ^ 12 ^ 13 ^
SP1: - - - - - -
SP2: - - - - - - -
SP3: - - - -
SP4: - - - - - - - - - -
SP5: - - - - - - - -
SP6: - - - - - - - - - - -
SP7: - - - - - - - - - - - -
SP8: - - - - - - - - -
SP9: - - - - - - - - - -
SP10: - - - - - - - -
SP11: - - - - - -
SP12: - -
SP13:
SP14: - - -
SP15:

ExUns: 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b · 19c
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for RNF38 Gene

GeneLoc Exon Structure for
RNF38
ECgene alternative splicing isoforms for
RNF38

Expression for RNF38 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNF38 Gene

Protein differential expression in normal tissues from HIPED for RNF38 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RNF38 Gene



Protein tissue co-expression partners for RNF38 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RNF38 Gene:

RNF38

SOURCE GeneReport for Unigene cluster for RNF38 Gene:

Hs.333503

mRNA Expression by UniProt/SwissProt for RNF38 Gene:

Q9H0F5-RNF38_HUMAN
Tissue specificity: Widely expressed with highest levels in testis.

Evidence on tissue expression from TISSUES for RNF38 Gene

  • Nervous system(4.8)
  • Intestine(4.2)
genes like me logo Genes that share expression patterns with RNF38: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNF38 Gene

Orthologs for RNF38 Gene

This gene was present in the common ancestor of animals.

Orthologs for RNF38 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RNF38 34 35
  • 99.81 (n)
oppossum
(Monodelphis domestica)
Mammalia RNF38 35
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RNF38 34 35
  • 96.68 (n)
cow
(Bos Taurus)
Mammalia RNF38 34 35
  • 95.68 (n)
mouse
(Mus musculus)
Mammalia Rnf38 34 16 35
  • 93.65 (n)
rat
(Rattus norvegicus)
Mammalia Rnf38 34
  • 93.36 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RNF38 35
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves RNF38 34 35
  • 81.04 (n)
lizard
(Anolis carolinensis)
Reptilia RNF38 35
  • 96 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rnf38 34
  • 81.03 (n)
Str.10151 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.24562 34
zebrafish
(Danio rerio)
Actinopterygii si:dkey-20n3.1 34
  • 70.92 (n)
RNF38 35
  • 57 (a)
OneToOne
wufa94e11 34
fruit fly
(Drosophila melanogaster)
Insecta mura 35
  • 14 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5812 34
Species where no ortholog for RNF38 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • 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)
  • 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 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RNF38 Gene

ENSEMBL:
Gene Tree for RNF38 (if available)
TreeFam:
Gene Tree for RNF38 (if available)

Paralogs for RNF38 Gene

Paralogs for RNF38 Gene

(1) SIMAP similar genes for RNF38 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with RNF38: view

Variants for RNF38 Gene

Sequence variations from dbSNP and Humsavar for RNF38 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs1000017056 -- 36,419,275(+) CATTT(G/T)CCATC intron-variant
rs1000056828 -- 36,484,128(+) TCTAC(G/T)GGGGA intron-variant
rs1000073931 -- 36,460,464(+) ATCAC(C/G)AAGAA intron-variant
rs1000076679 -- 36,471,873(+) TACAG(A/G)TGAGC intron-variant, upstream-variant-2KB
rs1000081663 -- 36,481,939(+) AGGAA(A/G)AGAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RNF38 Gene

Variant ID Type Subtype PubMed ID
dgv12665n54 CNV gain 21841781
dgv12666n54 CNV gain+loss 21841781
dgv12667n54 CNV gain 21841781
dgv12668n54 CNV loss 21841781
dgv3986n106 CNV deletion 24896259
dgv3987n106 CNV deletion 24896259
dgv483e215 CNV deletion 23714750
esv1684027 CNV deletion 17803354
esv2453594 CNV deletion 19546169
esv27332 CNV gain 19812545
esv2738421 CNV deletion 23290073
esv2738422 CNV deletion 23290073
esv2738423 CNV deletion 23290073
esv2738424 CNV deletion 23290073
esv3125348 CNV deletion 24192839
esv3268051 CNV deletion 24192839
esv33302 CNV loss 17666407
esv34080 CNV loss 18971310
esv3544815 CNV deletion 23714750
esv3620392 CNV loss 21293372
esv3856 CNV loss 18987735
nsv1017711 CNV gain 25217958
nsv1125318 OTHER inversion 24896259
nsv416514 CNV deletion 16902084
nsv499545 CNV loss 21111241
nsv511432 CNV loss 21212237
nsv512099 CNV loss 21212237
nsv614185 CNV loss 21841781
nsv614188 CNV loss 21841781
nsv6529 CNV insertion 18451855
nsv7420 OTHER inversion 18451855
nsv821197 CNV deletion 20802225
nsv824914 CNV gain 20364138
nsv824915 CNV gain 20364138
nsv824916 CNV loss 20364138
nsv824917 CNV gain+loss 20364138
nsv957113 CNV deletion 24416366

Variation tolerance for RNF38 Gene

Residual Variation Intolerance Score: 6.57% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.39; 8.52% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RNF38 Gene

Human Gene Mutation Database (HGMD)
RNF38
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNF38

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNF38 Gene

Disorders for RNF38 Gene

Relevant External Links for RNF38

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RNF38

No disorders were found for RNF38 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RNF38 Gene

Publications for RNF38 Gene

  1. RNF38 encodes a nuclear ubiquitin protein ligase that modifies p53. (PMID: 23973461) Sheren J.E. … Kassenbrock C.K. (Biochem. Biophys. Res. Commun. 2013) 3 4 64
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  3. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray S.J. … Dunham I. (Nature 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. Cloning and characterization of a novel human gene RNF38 encoding a conserved putative protein with a RING finger domain. (PMID: 12074600) Eisenberg I. … Mitrani-Rosenbaum S. (Biochem. Biophys. Res. Commun. 2002) 3 4 64

Products for RNF38 Gene

Sources for RNF38 Gene

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