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

Gene ID: 127544, updated on 24-Nov-2020

Summary

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
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

Genomic context

See RNF19B in Genome Data Viewer
Location:
1p35.1
Exon count:
10
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (32932498..32965266, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (33402050..33430467, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene hippocalcin Neighboring gene uncharacterized LOC105378632 Neighboring gene transmembrane protein 54 Neighboring gene metallothionein-1E pseudogene Neighboring gene ribosomal protein L18a pseudogene 4 Neighboring gene ribosomal protein S2 pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ90005

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin binding IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin conjugating enzyme binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
positive regulation of proteasomal ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein autoubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein polyubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein polyubiquitination TAS
Traceable Author Statement
more info
 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytolytic granule IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
ubiquitin ligase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001127361.3NP_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:187251
    IBR; In Between Ring fingers
    pfam01485
    Location:282320
    IBR; IBR domain, a half RING-finger domain
    pfam13639
    Location:118166
    zf-RING_2; Ring finger domain
    cl00570
    Location:346435
    AzlC; AzlC protein
  2. NM_001300826.2NP_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, ENST00000235150.4
    Conserved Domains (4) summary
    smart00647
    Location:187251
    IBR; In Between Ring fingers
    pfam01485
    Location:282320
    IBR; IBR domain, a half RING-finger domain
    pfam13639
    Location:118166
    zf-RING_2; Ring finger domain
    cl00570
    Location:346435
    AzlC; AzlC protein
  3. NM_153341.4NP_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
    Q6ZMZ0
    Related
    ENSP00000362555.7, ENST00000373456.11
    Conserved Domains (4) summary
    smart00647
    Location:187251
    IBR; In Between Ring fingers
    pfam01485
    Location:283321
    IBR; IBR domain, a half RING-finger domain
    pfam13639
    Location:118166
    zf-RING_2; Ring finger domain
    cl00570
    Location:347436
    AzlC; AzlC protein

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    32932498..32965266 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006710356.2XP_006710419.1  E3 ubiquitin-protein ligase RNF19B isoform X1

    See identical proteins and their annotated locations for XP_006710419.1

    UniProtKB/Swiss-Prot
    Q6ZMZ0
    Conserved Domains (4) summary
    smart00647
    Location:187251
    IBR; In Between Ring fingers
    pfam01485
    Location:283321
    IBR; IBR domain, a half RING-finger domain
    pfam13639
    Location:118166
    zf-RING_2; Ring finger domain
    cl00570
    Location:347436
    AzlC; AzlC protein
  2. XM_006710357.3XP_006710420.1  E3 ubiquitin-protein ligase RNF19B isoform X2

    Conserved Domains (4) summary
    smart00647
    Location:187251
    IBR; In Between Ring fingers
    pfam01485
    Location:283321
    IBR; IBR domain, a half RING-finger domain
    pfam13639
    Location:118166
    zf-RING_2; Ring finger domain
    cl00570
    Location:347436
    AzlC; AzlC protein
  3. XM_006710358.3XP_006710421.1  E3 ubiquitin-protein ligase RNF19B isoform X3

    Conserved Domains (4) summary
    smart00647
    Location:187251
    IBR; In Between Ring fingers
    pfam01485
    Location:283321
    IBR; IBR domain, a half RING-finger domain
    pfam13639
    Location:118166
    zf-RING_2; Ring finger domain
    cl00570
    Location:347436
    AzlC; AzlC protein
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