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    RNF19B ring finger protein 19B [ Homo sapiens (human) ]

    Gene ID: 127544, updated on 5-Mar-2024

    Summary

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    Official Symbol
    RNF19Bprovided by HGNC
    Official Full Name
    ring finger protein 19Bprovided by HGNC
    Primary source
    HGNC:HGNC:26886
    See related
    Ensembl:ENSG00000116514 MIM:610872; AllianceGenome:HGNC:26886
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NKLAM; IBRDC3
    Summary
    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]
    Expression
    Broad expression in testis (RPKM 31.7), bone marrow (RPKM 15.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RNF19B in Genome Data Viewer
    Location:
    1p35.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32929036..32964809, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (32788820..32824591, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (33402050..33430410, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33361017-33361615 Neighboring gene hippocalcin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 612 Neighboring gene uncharacterized LOC105378632 Neighboring gene transmembrane protein 54 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33390633-33391176 Neighboring gene Sharpr-MPRA regulatory region 2329 Neighboring gene NANOG hESC enhancer GRCh37_chr1:33413154-33413655 Neighboring gene metallothionein-1E-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 613 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:33430005-33430509 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:33446166-33447365 Neighboring gene ribosomal protein L18a pseudogene 4 Neighboring gene ribosomal protein S2 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Natural Killer Lytic-Associated Molecule (NKLAM): An E3 Ubiquitin Ligase With an Integral Role in Innate Immunity. Lawrence DW, et al. Front Physiol, 2020. PMID 33192571, Free PMC Article
    2. Natural killer lytic-associated molecule plays a role in controlling tumor dissemination and metastasis. Hoover RG, et al. Front Immunol, 2012. PMID 23269922, Free PMC Article
    3. Gene structure of human and mouse NKLAM, a gene associated with cellular cytotoxicity. Portis T, et al. Immunogenetics, 2000 Jun. PMID 10912506
    4. NK lytic-associated molecule: a novel gene selectively expressed in cells with cytolytic function. Kozlowski M, et al. J Immunol, 1999 Aug 15. PMID 10438909
    5. E3 ubiquitin ligase NKLAM is a macrophage phagosome protein and plays a role in bacterial killing. Lawrence DW, et al. Cell Immunol, 2012 Sep. PMID 23085241, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. NKLAM is a positive regulator of STAT1-mediated transcriptional activity and is an important component of the innate immune response.
      Title: E3 ubiquitin ligase NKLAM ubiquitinates STAT1 and positively regulates STAT1-mediated transcriptional activity.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ90005

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin conjugating enzyme binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin protein ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in natural killer cell mediated cytotoxicity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein autoubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytolytic granule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of ubiquitin ligase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase RNF19B
    Names
    IBR domain-containing protein 3
    natural killer lytic-associated molecule
    NP_001120833.1
    NP_001287755.1
    NP_699172.2
    XP_006710419.1
    XP_006710420.1
    XP_006710421.1
    XP_047301514.1
    XP_054190316.1
    XP_054190317.1
    XP_054190318.1
    XP_054190319.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001127361.3 → NP_001120833.1  E3 ubiquitin-protein ligase RNF19B isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, and another alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is shorter than isoform a.
      Source sequence(s)
      AK074486, AK131439, AL031602, BC062374, DA630289
      Consensus CDS
      CCDS44107.1
      UniProtKB/Swiss-Prot
      Q6ZMZ0
      Related
      ENSP00000349482.5, ENST00000356990.9
      Conserved Domains (4) summary
      smart00647
      Location:187 → 251
      IBR; In Between Ring fingers
      pfam01485
      Location:282 → 320
      IBR; IBR domain, a half RING-finger domain
      pfam13639
      Location:118 → 166
      zf-RING_2; Ring finger domain
      cl00570
      Location:346 → 435
      AzlC; AzlC protein

    2. NM_001300826.2 → NP_001287755.1  E3 ubiquitin-protein ligase RNF19B isoform c

      See identical proteins and their annotated locations for NP_001287755.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AK074486, AL031602, BC113560, BC143687, DA630289
      Consensus CDS
      CCDS72754.1
      UniProtKB/Swiss-Prot
      Q6ZMZ0
      Related
      ENSP00000235150.4, ENST00000235150.5
      Conserved Domains (4) summary
      smart00647
      Location:187 → 251
      IBR; In Between Ring fingers
      pfam01485
      Location:282 → 320
      IBR; IBR domain, a half RING-finger domain
      pfam13639
      Location:118 → 166
      zf-RING_2; Ring finger domain
      cl00570
      Location:346 → 435
      AzlC; AzlC protein

    3. NM_153341.4 → NP_699172.2  E3 ubiquitin-protein ligase RNF19B isoform a

      See identical proteins and their annotated locations for NP_699172.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AK074486, AL031602, BC113560, DA630289
      Consensus CDS
      CCDS372.2
      UniProtKB/Swiss-Prot
      B7ZLB2, E9PAW6, G3XA82, Q0VG77, Q5TH44, Q5TH45, Q6P6A4, Q6ZMZ0, Q8N2S8, Q8WUF3
      Related
      ENSP00000362555.7, ENST00000373456.11
      Conserved Domains (4) summary
      smart00647
      Location:187 → 251
      IBR; In Between Ring fingers
      pfam01485
      Location:283 → 321
      IBR; IBR domain, a half RING-finger domain
      pfam13639
      Location:118 → 166
      zf-RING_2; Ring finger domain
      cl00570
      Location:347 → 436
      AzlC; AzlC protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      32929036..32964809 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006710356.3 → XP_006710419.1  E3 ubiquitin-protein ligase RNF19B isoform X1

      See identical proteins and their annotated locations for XP_006710419.1

      UniProtKB/Swiss-Prot
      B7ZLB2, E9PAW6, G3XA82, Q0VG77, Q5TH44, Q5TH45, Q6P6A4, Q6ZMZ0, Q8N2S8, Q8WUF3
      Conserved Domains (4) summary
      smart00647
      Location:187 → 251
      IBR; In Between Ring fingers
      pfam01485
      Location:283 → 321
      IBR; IBR domain, a half RING-finger domain
      pfam13639
      Location:118 → 166
      zf-RING_2; Ring finger domain
      cl00570
      Location:347 → 436
      AzlC; AzlC protein

    2. XM_047445558.1 → XP_047301514.1  E3 ubiquitin-protein ligase RNF19B isoform X3

    3. XM_006710357.4 → XP_006710420.1  E3 ubiquitin-protein ligase RNF19B isoform X2

      Conserved Domains (4) summary
      smart00647
      Location:187 → 251
      IBR; In Between Ring fingers
      pfam01485
      Location:283 → 321
      IBR; IBR domain, a half RING-finger domain
      pfam13639
      Location:118 → 166
      zf-RING_2; Ring finger domain
      cl00570
      Location:347 → 436
      AzlC; AzlC protein

    4. XM_006710358.4 → XP_006710421.1  E3 ubiquitin-protein ligase RNF19B isoform X4

      Conserved Domains (4) summary
      smart00647
      Location:187 → 251
      IBR; In Between Ring fingers
      pfam01485
      Location:283 → 321
      IBR; IBR domain, a half RING-finger domain
      pfam13639
      Location:118 → 166
      zf-RING_2; Ring finger domain
      cl00570
      Location:347 → 436
      AzlC; AzlC protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      32788820..32824591 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334341.1 → XP_054190316.1  E3 ubiquitin-protein ligase RNF19B isoform X1

    2. XM_054334343.1 → XP_054190318.1  E3 ubiquitin-protein ligase RNF19B isoform X3

    3. XM_054334342.1 → XP_054190317.1  E3 ubiquitin-protein ligase RNF19B isoform X2

    4. XM_054334344.1 → XP_054190319.1  E3 ubiquitin-protein ligase RNF19B isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZMZ0.2 GenPept UniProtKB/Swiss-Prot:Q6ZMZ0

    Gene LinkOut

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