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UBR2 ubiquitin protein ligase E3 component n-recognin 2 [ Homo sapiens (human) ]

Gene ID: 23304, updated on 7-Oct-2018

Summary

Official Symbol
UBR2provided by HGNC
Official Full Name
ubiquitin protein ligase E3 component n-recognin 2provided by HGNC
Primary source
HGNC:HGNC:21289
See related
Ensembl:ENSG00000024048 MIM:609134; Vega:OTTHUMG00000014703
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
C6orf133; bA49A4.1; dJ242G1.1; dJ392M17.3
Summary
This gene encodes an E3 ubiquitin ligase of the N-end rule proteolytic pathway that targets proteins with destabilizing N-terminal residues for polyubiquitylation and proteasome-mediated degradation. Alternative splicing results in multiple transcript variants.[provided by RefSeq, May 2010]
Expression
Ubiquitous expression in thyroid (RPKM 7.8), spleen (RPKM 6.8) and 25 other tissues See more
Orthologs

Genomic context

See UBR2 in Genome Data Viewer
Location:
6p21.1
Exon count:
52
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (42563905..42693505)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (42531748..42661243)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene arf-GAP with GTPase, ANK repeat and PH domain-containing protein 2-like Neighboring gene ribosomal protein L36a pseudogene 5 Neighboring gene RNA, U6 small nuclear 890, pseudogene Neighboring gene peripherin 2 Neighboring gene ATPase H+ transporting V0 subunit c pseudogene 3

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study of smoking behaviours among Bangladeshi adults.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Pol gag-pol HIV-1 Pol is identified to have a physical interaction with ubiquitin protein ligase E3 component n-recognin 2 (UBR2) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
Vif vif HIV-1 Vif is identified to have a physical interaction with ubiquitin protein ligase E3 component n-recognin 2 (UBR2) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
Vpr vpr The interaction of Vpr with DDB1 facilitates the formation of complexes containing Cul4A-Roc1 E3 ubiquitin ligase. The association of Vpr with DDB1-containing E3 ligase mediates the degradation of UNG2 and SMUG1 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Adaptive Immune System, organism-specific biosystem (from REACTOME)
    Adaptive Immune System, organism-specific biosystemAdaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with...
  • Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystem (from REACTOME)
    Antigen processing: Ubiquitination & Proteasome degradation, organism-specific biosystemIntracellular foreign or aberrant host proteins are cleaved into peptide fragments of a precise size, such that they can be loaded on to class I MHC molecules and presented externally to cytotoxic T ...
  • Class I MHC mediated antigen processing & presentation, organism-specific biosystem (from REACTOME)
    Class I MHC mediated antigen processing & presentation, organism-specific biosystemMajor histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular b...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ36357, KIAA0349, MGC71112, DKFZp686C08114

Gene Ontology Provided by GOA

Function Evidence Code Pubs
leucine binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-protein transferase activity EXP
Inferred from Experiment
more info
PubMed 
ubiquitin-protein transferase activity TAS
Traceable Author Statement
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cellular response to leucine IDA
Inferred from Direct Assay
more info
PubMed 
chromatin silencing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin silencing ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H2A ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone H2A ubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
male meiosis I IEA
Inferred from Electronic Annotation
more info
 
male meiotic nuclear division ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of TOR signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transposition ISS
Inferred from Sequence or Structural Similarity
more info
 
protein polyubiquitination TAS
Traceable Author Statement
more info
 
protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
reciprocal meiotic recombination ISS
Inferred from Sequence or Structural Similarity
more info
 
spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
ubiquitin-dependent protein catabolic process via the N-end rule pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
chromatin IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
nucleus 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 UBR2
Names
RING-type E3 ubiquitin transferase UBR2
ubiquitin-protein ligase E3-alpha-2
ubiquitin-protein ligase E3-alpha-II
NP_001171730.1
NP_056070.1
XP_005249022.1
XP_005249023.1
XP_011512740.2
XP_011512741.1
XP_011512742.1
XP_011512743.1
XP_016866083.1
XP_016866084.1
XP_016866085.1
XP_016866086.1

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_001184801.1NP_001171730.1  E3 ubiquitin-protein ligase UBR2 isoform 2

    See identical proteins and their annotated locations for NP_001171730.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AL136223, AL391814, BC024217, DR003057
    Consensus CDS
    CCDS55001.1
    UniProtKB/Swiss-Prot
    Q8IWV8
    Related
    ENSP00000361994.2, OTTHUMP00000016403, ENST00000372903.6, OTTHUMT00000040555
    Conserved Domains (2) summary
    pfam02207
    Location:99166
    zf-UBR; Putative zinc finger in N-recognin (UBR box)
    pfam02617
    Location:222301
    ClpS; ATP-dependent Clp protease adaptor protein ClpS
  2. NM_001363705.1NP_001350634.1  E3 ubiquitin-protein ligase UBR2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon and contains another alternate in-frame exon of the same size compared to variant 1. The resulting isoform (3) is the same size but has an alternate internal sequence compared to isoform 1.
    Source sequence(s)
    AL049843, AL136223, AL391814
    Consensus CDS
    CCDS87404.1
    Conserved Domains (3) summary
    pfam02207
    Location:99166
    zf-UBR; Putative zinc finger in N-recognin (UBR box)
    pfam02617
    Location:222301
    ClpS; ATP-dependent Clp protease adaptor protein ClpS
    cd16686
    Location:11071222
    RING-H2_UBR2; RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-2 (UBR2) and similar proteins
  3. NM_015255.2NP_056070.1  E3 ubiquitin-protein ligase UBR2 isoform 1

    See identical proteins and their annotated locations for NP_056070.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK127310, AL049843, AL136223, AY061884, DR003057
    Consensus CDS
    CCDS4870.1
    UniProtKB/Swiss-Prot
    Q8IWV8
    UniProtKB/TrEMBL
    B3KXG6
    Related
    ENSP00000361990.1, OTTHUMP00000016405, ENST00000372899.5, OTTHUMT00000040558
    Conserved Domains (2) summary
    pfam02207
    Location:99166
    zf-UBR; Putative zinc finger in N-recognin (UBR box)
    pfam02617
    Location:222300
    ClpS; ATP-dependent Clp protease adaptor protein ClpS

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

    Range
    42563905..42693505
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005248965.4XP_005249022.1  E3 ubiquitin-protein ligase UBR2 isoform X4

    UniProtKB/Swiss-Prot
    Q8IWV8
    Related
    ENSP00000361992.1, OTTHUMP00000070741, ENST00000372901.1, OTTHUMT00000144880
    Conserved Domains (3) summary
    pfam02207
    Location:99166
    zf-UBR; Putative zinc finger in N-recognin (UBR box)
    pfam02617
    Location:222301
    ClpS; ATP-dependent Clp protease adaptor protein ClpS
    cd16686
    Location:11071222
    RING-H2_UBR2; RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-2 (UBR2) and similar proteins
  2. XM_017010597.1XP_016866086.1  E3 ubiquitin-protein ligase UBR2 isoform X6

  3. XM_017010595.1XP_016866084.1  E3 ubiquitin-protein ligase UBR2 isoform X3

  4. XM_017010594.1XP_016866083.1  E3 ubiquitin-protein ligase UBR2 isoform X2

  5. XM_011514438.2XP_011512740.2  E3 ubiquitin-protein ligase UBR2 isoform X1

  6. XM_017010596.1XP_016866085.1  E3 ubiquitin-protein ligase UBR2 isoform X5

  7. XM_005248966.3XP_005249023.1  E3 ubiquitin-protein ligase UBR2 isoform X9

    Conserved Domains (1) summary
    cl17238
    Location:404519
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  8. XM_011514440.1XP_011512742.1  E3 ubiquitin-protein ligase UBR2 isoform X7

    See identical proteins and their annotated locations for XP_011512742.1

    Conserved Domains (1) summary
    cl17238
    Location:611726
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  9. XM_011514439.1XP_011512741.1  E3 ubiquitin-protein ligase UBR2 isoform X7

    See identical proteins and their annotated locations for XP_011512741.1

    Conserved Domains (1) summary
    cl17238
    Location:611726
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
  10. XM_011514441.2XP_011512743.1  E3 ubiquitin-protein ligase UBR2 isoform X8

    Conserved Domains (1) summary
    cl17238
    Location:591706
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

RNA

  1. XR_001743285.1 RNA Sequence

  2. XR_001743284.2 RNA Sequence

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