UBP12 ubiquitin-specific protease 12 [Arabidopsis thaliana (thale cress)] - Gene

Summary

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Official Symbol: UBP12
Official Full Name: ubiquitin-specific protease 12
Primary source: TAIR:AT5G06600
Locus tag: AT5G06600
See related: Araport:AT5G06600
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Arabidopsis thaliana (ecotype: Columbia)
Lineage: Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Also known as: AtUBP12; F15M7.13; F15M7_13; ubiquitin-specific protease 12; UBIQUITIN-SPECIFIC PROTEASE 12
Summary: Encodes a ubiquitin-specific protease.
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Genomic context

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See UBP12 in Genome Data Viewer

Location:: chromosome: 5

Exon count:: 32

Sequence:: Chromosome: 5; NC_003076.8 (2019084..2028116, complement)

Chromosome 5 - NC_003076.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_003076.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Forward genetic approach identifies a phylogenetically conserved serine residue critical for the catalytic activity of UBIQUITIN-SPECIFIC PROTEASE 12 in Arabidopsis.
Title: Forward genetic approach identifies a phylogenetically conserved serine residue critical for the catalytic activity of UBIQUITIN-SPECIFIC PROTEASE 12 in Arabidopsis.
Deubiquitinating enzymes UBP12 and UBP13 stabilize the brassinosteroid receptor BRI1.
Title: Deubiquitinating enzymes UBP12 and UBP13 stabilize the brassinosteroid receptor BRI1.
Ubiquitin-specific proteases UBP12 and UBP13 promote shade avoidance response by enhancing PIF7 stability.
Title: Ubiquitin-specific proteases UBP12 and UBP13 promote shade avoidance response by enhancing PIF7 stability.
Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis.
Title: Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis.
UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2.
Title: UBP12 and UBP13 negatively regulate the activity of the ubiquitin-dependent peptidases DA1, DAR1 and DAR2.
UBP12/UBP13 deubiquitinate ORE1 to stabilize this transcription factor and promote its activity as a positive regulator for leaf senescence under nitrogen deficiency conditions.
Title: Arabidopsis ubiquitin-specific proteases UBP12 and UBP13 shape ORE1 levels during leaf senescence induced by nitrogen deficiency.
UBP12/13 are regulators of the RGF1-RGFR1-PLT1/2 signaling pathway and UBP12/13 can counteract RGF1-induced RGFR1 ubiquitination, stabilize RGFR1, and maintain root cell sensitivity to RGF1
Title: Regulation of the stability of RGF1 receptor by the ubiquitin-specific proteases UBP12/UBP13 is critical for root meristem maintenance.
UBP12 and UBP13 belong to an ancient gene family and represent plant homologues of metazoan USP7. Drosophila USP7 shares a function in heterochromatic gene repression with UBP12/13 and their homologue UBP26. In summary, USP7-like proteins are essential for gene silencing in diverse genomic contexts.
Title: H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system.
The Deubiquitinating Enzymes UBP12 and UBP13 Positively Regulate MYC2 Levels in Jasmonate Responses
Title: The Deubiquitinating Enzymes UBP12 and UBP13 Positively Regulate MYC2 Levels in Jasmonate Responses.
UBP12 and UBP13 proteins play important role in the control of the circadian clock and photoperiodic flowering.
Title: Ubiquitin-specific proteases UBP12 and UBP13 act in circadian clock and photoperiodic flowering regulation in Arabidopsis.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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NM_001125707.2

Supported by ESTs:

NM_120743.3

Supported by ESTs:

NM_180452.1

Supported by ESTs:

Gene Ontology Provided by TAIR

Function	Evidence Code	Pubs
enables cysteine-type deubiquitinase activity	IDA Inferred from Direct Assay more info	PubMed
enables cysteine-type deubiquitinase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within jasmonic acid mediated signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein deubiquitination	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IPI Inferred from Physical Interaction more info	PubMed
located_in cytosol	HDA more info	PubMed
located_in nucleus	IPI Inferred from Physical Interaction more info	PubMed
located_in nucleus	ISM Inferred from Sequence Model more info

General protein information

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Preferred Names: ubiquitin-specific protease 12

NP_001119179.1

ubiquitin-specific protease 12 (UBP12); FUNCTIONS IN: ubiquitin-specific protease activity, ubiquitin thiolesterase activity; INVOLVED IN: ubiquitin-dependent protein catabolic process; LOCATED IN: cellular_component unknown; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: TRAF-like (InterPro:IPR008974), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (InterPro:IPR018200), MATH (InterPro:IPR002083), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (InterPro:IPR001394), TRAF-type (InterPro:IPR013322); BEST Arabidopsis thaliana protein match is: ubiquitin-specific protease 13 (TAIR:AT3G11910.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).

NP_568171.1

ubiquitin-specific protease 12 (UBP12); FUNCTIONS IN: ubiquitin-specific protease activity, ubiquitin thiolesterase activity; INVOLVED IN: ubiquitin-dependent protein catabolic process; LOCATED IN: cellular_component unknown; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: TRAF-like (InterPro:IPR008974), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (InterPro:IPR018200), MATH (InterPro:IPR002083), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (InterPro:IPR001394), TRAF-type (InterPro:IPR013322); BEST Arabidopsis thaliana protein match is: ubiquitin-specific protease 13 (TAIR:AT3G11910.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).

NP_850783.1

ubiquitin-specific protease 12 (UBP12); FUNCTIONS IN: ubiquitin-specific protease activity, ubiquitin thiolesterase activity; INVOLVED IN: ubiquitin-dependent protein catabolic process; LOCATED IN: cellular_component unknown; EXPRESSED IN: 25 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: TRAF-like (InterPro:IPR008974), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (InterPro:IPR018200), MATH (InterPro:IPR002083), Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (InterPro:IPR001394), TRAF-type (InterPro:IPR013322); BEST Arabidopsis thaliana protein match is: ubiquitin-specific protease 13 (TAIR:AT3G11910.2); Has 8094 Blast hits to 7303 proteins in 267 species: Archae - 0; Bacteria - 2; Metazoa - 3813; Fungi - 1238; Plants - 1657; Viruses - 9; Other Eukaryotes - 1375 (source: NCBI BLink).

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_003076.8 Reference assembly

Range

2019084..2028116 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_120743.3 → NP_568171.1 ubiquitin-specific protease 12 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_568171.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q9C5K1, Q9FG10, Q9FPT1

UniProtKB/TrEMBL

A0A178UDR2, A0A5S9Y458

Conserved Domains (5) summary

COG5077
Location:57 → 1114

COG5077; Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

cd00121
Location:55 → 179

MATH; MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane ...

cd02659
Location:197 → 526

peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

pfam12436
Location:625 → 875

USP7_ICP0_bdg; ICP0-binding domain of Ubiquitin-specific protease 7

pfam14533
Location:884 → 1095

USP7_C2; Ubiquitin-specific protease C-terminal
NM_180452.1 → NP_850783.1 ubiquitin-specific protease 12 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_850783.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A178UC74

Conserved Domains (5) summary

COG5077
Location:56 → 1113

COG5077; Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

cd00121
Location:54 → 178

MATH; MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane ...

cd02659
Location:196 → 525

peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

pfam12436
Location:624 → 874

USP7_ICP0_bdg; ICP0-binding domain of Ubiquitin-specific protease 7

pfam14533
Location:883 → 1094

USP7_C2; Ubiquitin-specific protease C-terminal
NM_001125707.2 → NP_001119179.1 ubiquitin-specific protease 12 [Arabidopsis thaliana]

See identical proteins and their annotated locations for NP_001119179.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A178UDR2, A0A5S9Y458, F4K3X1

Conserved Domains (5) summary

cd00121
Location:55 → 179

MATH; MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane ...

cd02659
Location:197 → 526

peptidase_C19C; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

pfam00443
Location:199 → 521

UCH; Ubiquitin carboxyl-terminal hydrolase

pfam12436
Location:625 → 875

USP7_ICP0_bdg; ICP0-binding domain of Ubiquitin-specific protease 7

pfam14533
Location:884 → 983

USP7_C2; Ubiquitin-specific protease C-terminal