otud4 OTU deubiquitinase 4 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: otud4provided by ZNC
Official Full Name: OTU deubiquitinase 4provided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-5338
See related: Ensembl:ENSDARG00000077810 AllianceGenome:ZFIN:ZDB-GENE-030131-5338
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: wu:fd14a11; wu:fe11h08; zgc:165536
Summary: Predicted to enable Lys63-specific deubiquitinase activity and thiol-dependent deubiquitinase. Acts upstream of or within camera-type eye development; cerebellum development; and dorsal/ventral pattern formation. Orthologous to human OTUD4 (OTU deubiquitinase 4). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 23

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	23	NC_007134.7 (43668578..43692126)
105	previous assembly	GRCz10 (GCF_000002035.5)	23	NC_007134.6 (43868070..43890608)

Chromosome 23 - NC_007134.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

interruption of Bmp4 signaling by double knockdown of usp15 and otud4 reduced the ventralized effects in tsc22d3-overexpressing embryos
Title: Zebrafish transforming growth factor-β-stimulated clone 22 domain 3 (TSC22D3) plays critical roles in Bmp-dependent dorsoventral patterning via two deubiquitylating enzymes Usp15 and Otud4.

Submit: New GeneRIF Correction

General gene information

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Markers

fi09b08.x1 (e-PCR)
- UniSTS:196733

fe11h08.x1 (e-PCR)
- UniSTS:196089

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables K63-linked deubiquitinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cysteine-type deubiquitinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cysteine-type deubiquitinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within camera-type eye development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cerebellum development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cerebellum development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within dorsal/ventral pattern formation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in negative regulation of interleukin-1-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of toll-like receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein deubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of protein K48-linked deubiquitination	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: OTU domain-containing protein 4

Names: OTU domain containing 4 protein; parp11

XP_001923008.5

EC 3.4.19.12

XP_005174208.2

EC 3.4.19.12

XP_017209010.2

EC 3.4.19.12

XP_021325426.1

EC 3.4.19.12

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_001312659.3 → NP_001299588.3 OTU domain-containing protein 4

Status: VALIDATED

Source sequence(s)

CABZ01058306, CU681840, FO704781

UniProtKB/TrEMBL

A0A8M1P7L2, A0A8M1QHT8

Conserved Domains (4) summary

cd04508
Location:293 → 340

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

pfam15320
Location:1306 → 1350

RAM; mRNA cap methylation, RNMT-activating mini protein

cl19932
Location:41 → 120

OTU; OTU-like cysteine protease

cl26464
Location:521 → 936

Atrophin-1; Atrophin-1 family

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007134.7 Reference GRCz11 Primary Assembly

Range

43668578..43692126

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017353521.2 → XP_017209010.2 OTU domain-containing protein 4 isoform X4

UniProtKB/TrEMBL

A0A8M6YXM8

Conserved Domains (2) summary

cd04508
Location:293 → 340

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

cl19932
Location:41 → 120

OTU; OTU-like cysteine protease
XM_001922973.7 → XP_001923008.5 OTU domain-containing protein 4 isoform X2

Related

ENSDARP00000098303.4, ENSDART00000112598.4

Conserved Domains (4) summary

cd04508
Location:293 → 340

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

pfam15320
Location:1306 → 1350

RAM; mRNA cap methylation, RNMT-activating mini protein

cl19932
Location:41 → 120

OTU; OTU-like cysteine protease

cl26464
Location:521 → 936

Atrophin-1; Atrophin-1 family
XM_021469751.1 → XP_021325426.1 OTU domain-containing protein 4 isoform X3

UniProtKB/TrEMBL

A0A8M1P7L2, A0A8M9PSY0

Conserved Domains (4) summary

cd04508
Location:293 → 340

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

pfam15320
Location:1305 → 1349

RAM; mRNA cap methylation, RNMT-activating mini protein

cl19932
Location:41 → 120

OTU; OTU-like cysteine protease

cl26464
Location:520 → 935

Atrophin-1; Atrophin-1 family
XM_005174151.4 → XP_005174208.2 OTU domain-containing protein 4 isoform X1

UniProtKB/TrEMBL

A0A8M1P7L2, A0A8M2BLE4

Conserved Domains (4) summary

cd04508
Location:293 → 340

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

pfam15320
Location:1311 → 1355

RAM; mRNA cap methylation, RNMT-activating mini protein

cl19932
Location:41 → 120

OTU; OTU-like cysteine protease

cl26464
Location:526 → 941

Atrophin-1; Atrophin-1 family