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

    Gene ID: 23304, updated on 2-Nov-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 L-leucine binding activity and ubiquitin protein ligase activity. Involved in several processes, including cellular response to L-leucine; protein K63-linked ubiquitination; and regulation of signal transduction. Predicted to be located in cytosol. Predicted to be part of chromatin and ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    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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    See UBR2 in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    52
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (42564029..42693505)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (42392486..42521935)
    RS_2024_09 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 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. 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
    2. Burden of rare coding variants in an Italian cohort of familial multiple sclerosis. Mascia E, et al. J Neuroimmunol, 2022 Jan 15. PMID 34922125
    3. Identification of a novel antibody associated with autoimmune pancreatitis. Frulloni L, et al. N Engl J Med, 2009 Nov 26. PMID 19940298
    4. 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
    5. 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

    See all (82) 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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    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 Variation Viewer (GRCh37.p13)

    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 H2A 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 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 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 positive regulation of T cell receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein K63-linked ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    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
    		  
    involved_in ubiquitin-dependent protein catabolic process via the N-end rule pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chromatin IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytoplasm IC
    Inferred by Curator
    more info
    		 PubMed 
    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_2024_08

    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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