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

Gene ID: 127544, updated on 27-Nov-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32929036..32964809, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (32788820..32824591, complement)
RS_2024_09 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. Gene structure of human and mouse NKLAM, a gene associated with cellular cytotoxicity. Portis T, et al. Immunogenetics, 2000 Jun. PMID 10912506
  2. 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
  3. 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
  4. 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
  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 (28) 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)

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 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_2024_08

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

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