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

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; 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

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_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.

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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 EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

D11S2921 (e-PCR)
- UniSTS:152074

RH45756 (e-PCR)
- UniSTS:29459

STS-N38966 (e-PCR)
- UniSTS:55594

L17705 (e-PCR)
- UniSTS:66091

D6S1227E (e-PCR)
- UniSTS:151102

RH26772 (e-PCR)
- UniSTS:84295

G20787 (e-PCR)
- UniSTS:59469

A006G20 (e-PCR)
- UniSTS:59470

RH16533 (e-PCR)
- UniSTS:16993

RH65639 (e-PCR)
- UniSTS:70498

D10S16 (e-PCR)
- UniSTS:155756

D15S1477 (e-PCR)
- UniSTS:474482

D1S1423 (e-PCR)
- UniSTS:149619

G35510 (e-PCR)
- UniSTS:44150

RH36338 (e-PCR)
- UniSTS:14456

RH80397 (e-PCR)
- UniSTS:91256

L17877 (e-PCR)
- UniSTS:61334

RH79035 (e-PCR)
- UniSTS:17053

RH103886 (e-PCR)
- UniSTS:98211

L17809 (e-PCR)
- UniSTS:39087

A002V07 (e-PCR)
- UniSTS:44979

RH46716 (e-PCR)
- UniSTS:76512

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
part_of 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

EC 2.3.2.27

NP_001350634.1

EC 2.3.2.27

NP_056070.1

EC 2.3.2.27

XP_005249023.1

EC 2.3.2.27

XP_011512740.2

EC 2.3.2.27

XP_011512742.1

EC 2.3.2.27

XP_011512743.1

EC 2.3.2.27

XP_016866083.1

EC 2.3.2.27

XP_016866086.1

EC 2.3.2.27

XP_047274449.1

EC 2.3.2.27

XP_047274450.1

EC 2.3.2.27

XP_047274451.1

EC 2.3.2.27

XP_054210833.1

EC 2.3.2.27

XP_054210834.1

EC 2.3.2.27

XP_054210835.1

EC 2.3.2.27

XP_054210836.1

EC 2.3.2.27

XP_054210837.1

EC 2.3.2.27

XP_054210838.1

EC 2.3.2.27

XP_054210839.1

EC 2.3.2.27

XP_054210840.1

EC 2.3.2.27

XP_054210841.1

EC 2.3.2.27

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)

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
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
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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

42564029..42693505

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017010594.2 → XP_016866083.1 E3 ubiquitin-protein ligase UBR2 isoform X2
XM_011514438.3 → XP_011512740.2 E3 ubiquitin-protein ligase UBR2 isoform X1
XM_047418493.1 → XP_047274449.1 E3 ubiquitin-protein ligase UBR2 isoform X3
XM_017010597.2 → XP_016866086.1 E3 ubiquitin-protein ligase UBR2 isoform X4
XM_047418494.1 → XP_047274450.1 E3 ubiquitin-protein ligase UBR2 isoform X7
XM_047418495.1 → XP_047274451.1 E3 ubiquitin-protein ligase UBR2 isoform X9
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
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
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