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Aliases for RNF19B Gene

Aliases for RNF19B Gene

  • Ring Finger Protein 19B 2 3 5
  • Natural Killer Lytic-Associated Molecule 3 4
  • E3 Ubiquitin-Protein Ligase RNF19B 3 4
  • IBR Domain-Containing Protein 3 3 4
  • IBRDC3 3 4
  • NKLAM 3 4
  • RING Finger Protein 19B 4
  • IBR Domain Containing 3 2
  • EC 2.3.2.31 4
  • EC 6.3.2 56

External Ids for RNF19B Gene

Previous HGNC Symbols for RNF19B Gene

  • IBRDC3

Previous GeneCards Identifiers for RNF19B Gene

  • GC01M033175
  • GC01M033402
  • GC01M031517

Summaries for RNF19B Gene

Entrez Gene Summary for RNF19B Gene

  • This gene encodes a multi-pass membrane protein containing two RING-type and one IBR-type zinc finger motifs. The encoded protin is an E3 ubiquitin-protein ligase that plays a role in the cytotoxic effects of natural killer (NK) cells. Alternative splicing results in multiple transcript variants. There are pseudogenes for this gene on chromosomes X and Y in a possible pseudoautosomal region. [provided by RefSeq, Jul 2014]

GeneCards Summary for RNF19B Gene

RNF19B (Ring Finger Protein 19B) is a Protein Coding gene. Among its related pathways are Innate Immune System and Class I MHC mediated antigen processing and presentation. Gene Ontology (GO) annotations related to this gene include ligase activity. An important paralog of this gene is RNF19A.

UniProtKB/Swiss-Prot for RNF19B Gene

  • E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates, such as UCKL1 (PubMed:16709802, PubMed:27485036). Involved in the cytolytic activity of natural killer cells and cytotoxic T-cells (PubMed:10438909). Protects against staurosporin-induced cell death (PubMed:27485036).

Additional gene information for RNF19B Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RNF19B Gene

Genomics for RNF19B Gene

GeneHancer (GH) Regulatory Elements for RNF19B Gene

Promoters and enhancers for RNF19B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RNF19B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RNF19B gene promoter:
  • AML1a
  • Chx10
  • COMP1
  • HNF-4alpha2
  • Nkx2-5
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4

Genomic Locations for RNF19B Gene

Genomic Locations for RNF19B Gene
chr1:32,932,498-32,965,266
(GRCh38/hg38)
Size:
32,769 bases
Orientation:
Minus strand
chr1:33,402,046-33,430,286
(GRCh37/hg19)
Size:
28,241 bases
Orientation:
Minus strand

Genomic View for RNF19B Gene

Genes around RNF19B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNF19B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNF19B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNF19B Gene

Proteins for RNF19B Gene

  • Protein details for RNF19B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6ZMZ0-RN19B_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase RNF19B
    Protein Accession:
    Q6ZMZ0
    Secondary Accessions:
    • B7ZLB2
    • E9PAW6
    • G3XA82
    • Q0VG77
    • Q5TH44
    • Q5TH45
    • Q6P6A4
    • Q8N2S8
    • Q8WUF3

    Protein attributes for RNF19B Gene

    Size:
    732 amino acids
    Molecular mass:
    77925 Da
    Quaternary structure:
    • Interacts with UBE2L3, UBE2L6 and UCKL1.
    SequenceCaution:
    • Sequence=AAI13561.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI43688.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=EAX07490.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for RNF19B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RNF19B Gene

Selected DME Specific Peptides for RNF19B Gene

Q6ZMZ0:
  • VCGCEFCWLCMKEISDLHYLSPSGCTFWGKKPWSRKKK
  • RLEVQADVQKE
  • DPDCRWCPAPDCG
  • TEFCYHCKQIWHPNQTCD
  • AYIIKMNDGSCNHMTC
  • SKHKRNLAI
  • SLCRGGGCGV
  • DDIKPCPRC
  • PAMVIGIPVY
  • KYEEFMLRR

Post-translational modifications for RNF19B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RNF19B Gene

Domains & Families for RNF19B Gene

Gene Families for RNF19B Gene

Protein Domains for RNF19B Gene

Suggested Antigen Peptide Sequences for RNF19B Gene

GenScript: Design optimal peptide antigens:
  • RNF19B protein (B7ZLB2_HUMAN)
  • RING finger protein 19B (RN19B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q6ZMZ0

UniProtKB/Swiss-Prot:

RN19B_HUMAN :
  • The first IBR-type zinc finger is the most crucial for interaction with UBE2L3, UBE2L6 and UCKL1.
  • Belongs to the RBR family. RNF19 subfamily.
Domain:
  • The first IBR-type zinc finger is the most crucial for interaction with UBE2L3, UBE2L6 and UCKL1.
  • Members of the RBR family are atypical E3 ligases. They interact with the E2 conjugating enzyme UBE2L3 and function like HECT-type E3 enzymes: they bind E2s via the first RING domain, but require an obligate trans-thiolation step during the ubiquitin transfer, requiring a conserved cysteine residue in the second RING domain.
Family:
  • Belongs to the RBR family. RNF19 subfamily.
genes like me logo Genes that share domains with RNF19B: view

Function for RNF19B Gene

Molecular function for RNF19B Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates, such as UCKL1 (PubMed:16709802, PubMed:27485036). Involved in the cytolytic activity of natural killer cells and cytotoxic T-cells (PubMed:10438909). Protects against staurosporin-induced cell death (PubMed:27485036).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N(6)-ubiquitinyl-L-lysine.; EC=2.3.2.31; Evidence=. ;.
UniProtKB/Swiss-Prot Induction:
In natural killer cells, by IFNB1/IFN-beta and IL2/interleukin-2 (at protein level) (PubMed:10438909). Up-regulated by endoplasmic reticulum (ER) stress triggered by thapsigargin or tunicamycin (PubMed:27485036).

Enzyme Numbers (IUBMB) for RNF19B Gene

Phenotypes From GWAS Catalog for RNF19B Gene

Gene Ontology (GO) - Molecular Function for RNF19B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IEA --
GO:0005515 protein binding IPI 16709802
GO:0016740 transferase activity IEA --
GO:0031624 ubiquitin conjugating enzyme binding IBA 21873635
GO:0043130 ubiquitin binding IDA 27485036
genes like me logo Genes that share ontologies with RNF19B: view
genes like me logo Genes that share phenotypes with RNF19B: view

Animal Models for RNF19B Gene

MGI Knock Outs for RNF19B:

Animal Model Products

CRISPR Products

miRNA for RNF19B Gene

miRTarBase miRNAs that target RNF19B

Clone Products

  • Applied Biological Materials (abm): Clones for RNF19B - Now 50% OFF >
  • * RNF19B as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * RNF19B tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RNF19B Gene

Localization for RNF19B Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNF19B Gene

Cytoplasmic granule membrane; Multi-pass membrane protein. Endoplasmic reticulum membrane; Multi-pass membrane protein.

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 RNF19B gene
Compartment Confidence
endoplasmic reticulum 5
cytosol 4
plasma membrane 3
lysosome 3
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RNF19B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000151 ubiquitin ligase complex IBA 21873635
GO:0005737 cytoplasm IBA 21873635
GO:0005783 endoplasmic reticulum IDA,IEA 27485036
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with RNF19B: view

Pathways & Interactions for RNF19B Gene

genes like me logo Genes that share pathways with RNF19B: view

UniProtKB/Swiss-Prot Q6ZMZ0-RN19B_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for RNF19B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000209 protein polyubiquitination IBA,TAS --
GO:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IBA 21873635
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with RNF19B: view

No data available for SIGNOR curated interactions for RNF19B Gene

Drugs & Compounds for RNF19B Gene

No Compound Related Data Available

Transcripts for RNF19B Gene

mRNA/cDNA for RNF19B Gene

Unigene Clusters for RNF19B Gene

Ring finger protein 19B:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for RNF19B - Now 50% OFF >
  • * RNF19B as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * RNF19B tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for RNF19B Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c
SP1:
SP2: -
SP3: - -

Relevant External Links for RNF19B Gene

GeneLoc Exon Structure for
RNF19B
ECgene alternative splicing isoforms for
RNF19B

Expression for RNF19B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNF19B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RNF19B Gene

This gene is overexpressed in Whole Blood (x5.1) and Testis (x4.9).

Protein differential expression in normal tissues from HIPED for RNF19B Gene

This gene is overexpressed in Liver (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RNF19B Gene



Protein tissue co-expression partners for RNF19B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RNF19B Gene:

RNF19B

SOURCE GeneReport for Unigene cluster for RNF19B Gene:

Hs.591504

mRNA Expression by UniProt/SwissProt for RNF19B Gene:

Q6ZMZ0-RN19B_HUMAN
Tissue specificity: Expressed specifically in natural killer cells, activated macrophages and cytotoxic T-cells (PubMed:10438909). Present in natural killer cells (at protein level) (PubMed:10912506). Ubiquitously expressed with high expression in testis (PubMed:27485036).

Evidence on tissue expression from TISSUES for RNF19B Gene

  • Kidney(4.4)
  • Blood(4.3)
  • Nervous system(4.3)
  • Stomach(2)
genes like me logo Genes that share expression patterns with RNF19B: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for RNF19B Gene

Orthologs for RNF19B Gene

This gene was present in the common ancestor of animals.

Orthologs for RNF19B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RNF19B 35 34
  • 99.57 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RNF19B 35 34
  • 93.98 (n)
OneToOne
cow
(Bos Taurus)
Mammalia RNF19B 35 34
  • 90.55 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rnf19b 17 35 34
  • 90.4 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RNF19B 35
  • 90 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RNF19B 35
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves RNF19B 35 34
  • 79.77 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RNF19B 35
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rnf19b 34
  • 74.05 (n)
Str.2343 34
zebrafish
(Danio rerio)
Actinopterygii rnf19b 35 34
  • 67.13 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y49F6B.9 35
  • 41 (a)
ManyToMany
C17H11.6 35
  • 29 (a)
ManyToMany
Species where no ortholog for RNF19B 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)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • wheat (Triticum aestivum)

Evolution for RNF19B Gene

ENSEMBL:
Gene Tree for RNF19B (if available)
TreeFam:
Gene Tree for RNF19B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RNF19B: view image

Paralogs for RNF19B Gene

Paralogs for RNF19B Gene

(1) SIMAP similar genes for RNF19B Gene using alignment to 4 proteins:

  • RN19B_HUMAN
  • B7ZLB2_HUMAN
  • E9PAW6_HUMAN
  • G3XA82_HUMAN
genes like me logo Genes that share paralogs with RNF19B: view

Variants for RNF19B Gene

Sequence variations from dbSNP and Humsavar for RNF19B Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000071009 -- 32,963,837(-) G/A intron_variant
rs1000084351 -- 32,957,566(-) G/A intron_variant
rs1000123025 -- 32,963,586(-) C/T intron_variant
rs1000186427 -- 32,963,707(-) G/C intron_variant
rs1000191161 -- 32,932,382(-) A/G downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for RNF19B Gene

Variant ID Type Subtype PubMed ID
esv2664245 CNV deletion 23128226
esv3560460 CNV deletion 23714750
esv3576805 CNV gain 25503493
esv3585679 CNV loss 21293372
nsv1075812 CNV deletion 25765185
nsv509169 CNV insertion 20534489
nsv834602 CNV loss 17160897

Variation tolerance for RNF19B Gene

Residual Variation Intolerance Score: 11.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.66; 31.84% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RNF19B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNF19B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNF19B Gene

Disorders for RNF19B Gene

Additional Disease Information for RNF19B

No disorders were found for RNF19B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RNF19B Gene

Publications for RNF19B Gene

  1. Genome-wide identification and gene expression profiling of ubiquitin ligases for endoplasmic reticulum protein degradation. (PMID: 27485036) Kaneko M … Nomura Y (Scientific reports 2016) 3 4 58
  2. NK lytic-associated molecule, involved in NK cytotoxic function, is an E3 ligase. (PMID: 16709802) Fortier JM … Kornbluth J (Journal of immunology (Baltimore, Md. : 1950) 2006) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58

Products for RNF19B Gene

Sources for RNF19B Gene

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