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

Gene ID: 23304, updated on 11-Apr-2024

Summary

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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; AllianceGenome:HGNC:21289
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
Enables leucine binding activity. Involved in cellular response to leucine and negative regulation of TOR signaling. Predicted to be located in cytosol. Predicted to be part of ubiquitin ligase complex. Predicted to be active in cytoplasm. Predicted to colocalize with chromatin. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 7.8), spleen (RPKM 6.8) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
6p21.1
Exon count:
52
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42564029..42693505)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42392486..42521935)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (42531767..42661243)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24556 Neighboring gene uncharacterized LOC124901317 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24559 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24561 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42571822-42572008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24562 Neighboring gene RNA, U6 small nuclear 890, pseudogene Neighboring gene MPRA-validated peak5809 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:42677933-42678518 Neighboring gene peripherin 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24563 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24565 Neighboring gene ATPase H+ transporting V0 subunit c pseudogene 3

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. Burden of rare coding variants in an Italian cohort of familial multiple sclerosis. Mascia E, et al. J Neuroimmunol, 2022 Jan 15. PMID 34922125
  2. The E3 ligase UBR2 regulates cell death under caspase deficiency via Erk/MAPK pathway. Villa E, et al. Cell Death Dis, 2020 Dec 8. PMID 33288741, Free PMC Article
  3. Association of single nucleotide polymorphisms in UBR2 gene with idiopathic aspermia or oligospermia in Sichuan, China. Ma TJ, et al. Andrologia, 2016 Dec. PMID 26940145
  4. Single nucleotide polymorphism in the UBR2 gene may be a genetic risk factor for Japanese patients with azoospermia by meiotic arrest. Miyamoto T, et al. J Assist Reprod Genet, 2011 Aug. PMID 21573678, Free PMC Article
  5. Identification of a novel antibody associated with autoimmune pancreatitis. Frulloni L, et al. N Engl J Med, 2009 Nov 26. PMID 19940298

See all (76) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The phosphatase DUSP22 inhibits UBR2-mediated K63-ubiquitination and activation of Lck downstream of TCR signalling.
    Title: The phosphatase DUSP22 inhibits UBR2-mediated K63-ubiquitination and activation of Lck downstream of TCR signalling.
  2. Burden of rare coding variants in an Italian cohort of familial multiple sclerosis.
    Title: Burden of rare coding variants in an Italian cohort of familial multiple sclerosis.
  3. The E3 ligase UBR2 regulates cell death under caspase deficiency via Erk/MAPK pathway.
    Title: The E3 ligase UBR2 regulates cell death under caspase deficiency via Erk/MAPK pathway.
  4. There was a significant difference between the oligospermia men (oligospermia group) and the fertile men (control group) observed in this research that could indicate that the combined AT-TC-CC genotype in the UBR2 gene (rs16895863, rs373341, rs3749897 respectively) is a possible risk of idiopathic oligospermia for men in Sichuan, China.
    Title: Association of single nucleotide polymorphisms in UBR2 gene with idiopathic aspermia or oligospermia in Sichuan, China.
  5. The c.1,066A>T variant in the UBR2 gene is associated with increased susceptibility to azoospermia caused by meiotic arrest.
    Title: Single nucleotide polymorphism in the UBR2 gene may be a genetic risk factor for Japanese patients with azoospermia by meiotic arrest.
  6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  7. Study provides functional data for the mouse ubiquitin protein ligase E3 component n-recognin 2 protein.
    Title: Female lethality and apoptosis of spermatocytes in mice lacking the UBR2 ubiquitin ligase of the N-end rule pathway.
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

EBI GWAS Catalog

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

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

HIV-1 interactions

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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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ36357, KIAA0349, MGC71112, DKFZp686C08114

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables L-leucine binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone ubiquitin ligase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cellular response to L-leucine IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in heterochromatin formation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in male meiosis I IEA
Inferred from Electronic Annotation
more info
  
involved_in male meiotic nuclear division ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of TOR signaling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein ubiquitination IEA
Inferred from Electronic Annotation
more info
  
involved_in reciprocal meiotic recombination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in retrotransposon silencing ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of chromatin IEA
Inferred from Electronic Annotation
more info
  
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in nucleus 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 UBR2
Names
RING-type E3 ubiquitin transferase UBR2
ubiquitin-protein ligase E3-alpha-2
ubiquitin-protein ligase E3-alpha-II
NP_001171730.1
NP_001350634.1
NP_056070.1
XP_005249023.1
XP_011512740.2
XP_011512742.1
XP_011512743.1
XP_016866083.1
XP_016866086.1
XP_047274449.1
XP_047274450.1
XP_047274451.1
XP_054210833.1
XP_054210834.1
XP_054210835.1
XP_054210836.1
XP_054210837.1
XP_054210838.1
XP_054210839.1
XP_054210840.1
XP_054210841.1

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_001184801.2 → NP_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, ENST00000372903.6
    Conserved Domains (2) summary
    pfam02207
    Location:99 → 166
    zf-UBR; Putative zinc finger in N-recognin (UBR box)
    pfam02617
    Location:222 → 301
    ClpS; ATP-dependent Clp protease adaptor protein ClpS

  2. NM_001363705.2 → NP_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
    Related
    ENSP00000361992.1, ENST00000372901.2
    Conserved Domains (3) summary
    pfam02207
    Location:99 → 166
    zf-UBR; Putative zinc finger in N-recognin (UBR box)
    pfam02617
    Location:222 → 301
    ClpS; ATP-dependent Clp protease adaptor protein ClpS
    cd16686
    Location:1107 → 1222
    RING-H2_UBR2; RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-2 (UBR2) and similar proteins

  3. NM_015255.3 → NP_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
    O15057, Q4VXK2, Q5TFH6, Q6P2I2, Q6ZUD0, Q8IWV8
    Related
    ENSP00000361990.1, ENST00000372899.6
    Conserved Domains (2) summary
    pfam02207
    Location:99 → 166
    zf-UBR; Putative zinc finger in N-recognin (UBR box)
    pfam02617
    Location:222 → 300
    ClpS; ATP-dependent Clp protease adaptor protein ClpS

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    42564029..42693505
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010594.2 → XP_016866083.1  E3 ubiquitin-protein ligase UBR2 isoform X2

  2. XM_011514438.3 → XP_011512740.2  E3 ubiquitin-protein ligase UBR2 isoform X1

  3. XM_047418493.1 → XP_047274449.1  E3 ubiquitin-protein ligase UBR2 isoform X3

  4. XM_017010597.2 → XP_016866086.1  E3 ubiquitin-protein ligase UBR2 isoform X4

  5. XM_047418494.1 → XP_047274450.1  E3 ubiquitin-protein ligase UBR2 isoform X7

  6. XM_047418495.1 → XP_047274451.1  E3 ubiquitin-protein ligase UBR2 isoform X9

  7. XM_011514440.2 → XP_011512742.1  E3 ubiquitin-protein ligase UBR2 isoform X5

    See identical proteins and their annotated locations for XP_011512742.1

    UniProtKB/TrEMBL
    B4E215
    Conserved Domains (1) summary
    cl17238
    Location:611 → 726
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

  8. XM_011514441.3 → XP_011512743.1  E3 ubiquitin-protein ligase UBR2 isoform X6

    UniProtKB/TrEMBL
    B4E215
    Conserved Domains (1) summary
    cl17238
    Location:591 → 706
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

  9. XM_005248966.4 → XP_005249023.1  E3 ubiquitin-protein ligase UBR2 isoform X8

    Conserved Domains (1) summary
    cl17238
    Location:404 → 519
    RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    42392486..42521935
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354858.1 → XP_054210833.1  E3 ubiquitin-protein ligase UBR2 isoform X1

  2. XM_054354860.1 → XP_054210835.1  E3 ubiquitin-protein ligase UBR2 isoform X3

  3. XM_054354861.1 → XP_054210836.1  E3 ubiquitin-protein ligase UBR2 isoform X4

  4. XM_054354864.1 → XP_054210839.1  E3 ubiquitin-protein ligase UBR2 isoform X7

  5. XM_054354859.1 → XP_054210834.1  E3 ubiquitin-protein ligase UBR2 isoform X2

  6. XM_054354866.1 → XP_054210841.1  E3 ubiquitin-protein ligase UBR2 isoform X9

  7. XM_054354862.1 → XP_054210837.1  E3 ubiquitin-protein ligase UBR2 isoform X5

  8. XM_054354863.1 → XP_054210838.1  E3 ubiquitin-protein ligase UBR2 isoform X6

  9. XM_054354865.1 → XP_054210840.1  E3 ubiquitin-protein ligase UBR2 isoform X8

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IWV8.1 GenPept UniProtKB/Swiss-Prot:Q8IWV8

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