Ubr5 ubiquitin protein ligase E3 component n-recognin 5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Ubr5provided by RGD
Full Name: ubiquitin protein ligase E3 component n-recognin 5provided by RGD
Primary source: RGD:621236
See related: Ensembl:ENSRNOG00000006816 AllianceGenome:RGD:621236
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Dd5; Rat100
Summary: Enables protein domain specific binding activity and ubiquitin protein ligase activity. Involved in protein ubiquitination. Located in cytosol. Human ortholog(s) of this gene implicated in invasive ductal carcinoma. Orthologous to human UBR5 (ubiquitin protein ligase E3 component n-recognin 5). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Testes (RPKM 487.0), Heart (RPKM 391.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 7q22

Exon count:: 60

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	7	NC_086025.1 (71000197..71109841, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	7	NC_051342.1 (69115216..69224843, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	7	NC_005106.4 (76839661..76907441, complement) , (76789110..76835517, complement)

Chromosome 7 - NC_086025.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

UBR5 is a novel E3 ubiquitin ligase involved in skeletal muscle hypertrophy and recovery from atrophy.
Title: UBR5 is a novel E3 ubiquitin ligase involved in skeletal muscle hypertrophy and recovery from atrophy.
results confirm the role of the MLLE domain of UBR5 in substrate recruitment and suggest a potential role in regulating UBR5 ligase activity.
Title: The MLLE domain of the ubiquitin ligase UBR5 binds to its catalytic domain to regulate substrate binding.
PABC domains from the ubiquitin-protein isopeptide ligase HYD and poly(A)-binding protein
Title: Comparative peptide binding studies of the PABC domains from the ubiquitin-protein isopeptide ligase HYD and poly(A)-binding protein. Implications for HYD function.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW549941 (e-PCR)
- UniSTS:180748

RH126145 (e-PCR)
- UniSTS:162857

D7Rat24 (e-PCR), detects polymorphism
- UniSTS:228183

EST4E9 (e-PCR)
- UniSTS:263365

RH15795 (e-PCR)
- UniSTS:69326

RH129947 (e-PCR)
- UniSTS:213235

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables protein domain specific binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin protein ligase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables ubiquitin protein ligase activity	ISO Inferred from Sequence Orthology more info
enables ubiquitin-ubiquitin ligase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin-ubiquitin ligase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin-ubiquitin ligase activity	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA repair-dependent chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in DNA repair-dependent chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in DNA repair-dependent chromatin remodeling	ISS Inferred from Sequence or Structural Similarity more info
involved_in heterochromatin boundary formation	IEA Inferred from Electronic Annotation more info
involved_in heterochromatin boundary formation	ISO Inferred from Sequence Orthology more info
involved_in heterochromatin boundary formation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within negative regulation of interleukin-17 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein import into nucleus	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein import into nucleus	ISO Inferred from Sequence Orthology more info
involved_in progesterone receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in progesterone receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in protein K48-linked ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein K48-linked ubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein polyubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein polyubiquitination	ISO Inferred from Sequence Orthology more info
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of protein stability	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase UBR5

Names: E3 ubiquitin-protein ligase UBR5-like; E3 ubiquitin-protein ligase, HECT domain-containing 1; HECT-type E3 ubiquitin transferase UBR5; hyperplastic discs protein homolog; progestin-induced protein

NP_001406471.1

EC 2.3.2.26

XP_017450714.1

EC 2.3.2.26

XP_038936092.1

EC 2.3.2.26

XP_038936093.1

EC 2.3.2.26

XP_038936094.1

EC 2.3.2.26

XP_063118967.1

EC 2.3.2.26

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_001419542.1 → NP_001406471.1 E3 ubiquitin-protein ligase UBR5

Status: VALIDATED

Source sequence(s)

JAXUCZ010000007

UniProtKB/TrEMBL

A0A8I6ARZ1

Related

ENSRNOP00000097070.1, ENSRNOT00000115536.1

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086025.1 Reference GRCr8

Range

71000197..71109841 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039080165.2 → XP_038936093.1 E3 ubiquitin-protein ligase UBR5 isoform X3

UniProtKB/Swiss-Prot

F1LRS0, Q62671

Related

ENSRNOP00000009115.8

Conserved Domains (4) summary

smart00396
Location:1171 → 1238

ZnF_UBR1; Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway

smart00517
Location:2383 → 2446

PolyA; C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein

smart00119
Location:2494 → 2789

HECTc; Domain Homologous to E6-AP Carboxyl Terminus with

cd14423
Location:184 → 230

CUE_UBR5; CUE domain found in E3 ubiquitin-protein ligase UBR5 and similar proteins
XM_039080166.2 → XP_038936094.1 E3 ubiquitin-protein ligase UBR5 isoform X4

UniProtKB/Swiss-Prot

F1LRS0, Q62671

Conserved Domains (4) summary

smart00396
Location:1160 → 1227

ZnF_UBR1; Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway

smart00517
Location:2372 → 2435

PolyA; C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein

smart00119
Location:2483 → 2778

HECTc; Domain Homologous to E6-AP Carboxyl Terminus with

cd14423
Location:184 → 230

CUE_UBR5; CUE domain found in E3 ubiquitin-protein ligase UBR5 and similar proteins
XM_063262897.1 → XP_063118967.1 E3 ubiquitin-protein ligase UBR5 isoform X2
XM_039080164.2 → XP_038936092.1 E3 ubiquitin-protein ligase UBR5 isoform X1

UniProtKB/Swiss-Prot

F1LRS0, Q62671

Conserved Domains (4) summary

smart00396
Location:1177 → 1244

ZnF_UBR1; Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway

smart00517
Location:2389 → 2452

PolyA; C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein

smart00119
Location:2498 → 2793

HECTc; Domain Homologous to E6-AP Carboxyl Terminus with

cd14423
Location:184 → 230

CUE_UBR5; CUE domain found in E3 ubiquitin-protein ligase UBR5 and similar proteins
XM_017595225.3 → XP_017450714.1 E3 ubiquitin-protein ligase UBR5 isoform X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001191990.1: Suppressed sequence

Description

NM_001191990.1: This RefSeq was temporarily suppressed because currently there is not sufficient data to support this transcript.
NM_053989.1: Suppressed sequence

Description

NM_053989.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.