Cyld CYLD lysine 63 deubiquitinase [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Cyldprovided by RGD
Full Name: CYLD lysine 63 deubiquitinaseprovided by RGD
Primary source: RGD:1308346
See related: Ensembl:ENSRNOG00000014048 AllianceGenome:RGD:1308346
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Rp1; Rp1h; LRRGT00003
Summary: Predicted to enable several functions, including deubiquitinase activity; proline-rich region binding activity; and zinc ion binding activity. Predicted to be involved in several processes, including protein deubiquitination; regulation of organelle organization; and regulation of signal transduction. Predicted to act upstream of or within several processes, including positive regulation of T cell receptor signaling pathway; regulation of lymphocyte differentiation; and ripoptosome assembly involved in necroptotic process. Predicted to be located in ciliary tip and microtubule cytoskeleton. Predicted to be extrinsic component of cytoplasmic side of plasma membrane. Predicted to be part of cytosolic small ribosomal subunit. Predicted to be active in cytosol. Predicted to colocalize with cytoplasmic microtubule and midbody. Human ortholog(s) of this gene implicated in Brooke-Spiegler syndrome. Orthologous to human CYLD (CYLD lysine 63 deubiquitinase). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 144.8), Testes (RPKM 133.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19p11

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (34487491..34547311, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (18310632..18373696, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (19264984..19323817, complement)

Chromosome 19 - NC_086037.1 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?

LncRNA growth arrest specific transcript 5 inhibits the growth of pituitary neuroendocrine tumors via miR-27a-5p/cylindromatosis axis.
Title: LncRNA growth arrest specific transcript 5 inhibits the growth of pituitary neuroendocrine tumors via miR-27a-5p/cylindromatosis axis.
Beneficial effects of chlorogenic acid treatment on neuroinflammation after deep hypothermic circulatory arrest may be mediated through CYLD/NF-kappaB signaling.
Title: Beneficial effects of chlorogenic acid treatment on neuroinflammation after deep hypothermic circulatory arrest may be mediated through CYLD/NF-κB signaling.
Cylindromatosis coregulates the apoptosis and necroptosis of photoreceptor cells by regulating the ubiquitination of receptor-interacting protein 1 after retinal detachment.
Title: RNA Interference Reveals the Coregulatory Effects of Cylindromatosis on Apoptosis and Necroptosis of Photoreceptor Cells in Experimental Retinal Detachment.
CYLD contributes to the transdifferentiation of adventitial fibroblasts via deubiquitinating Nox4 and may play a role in vascular remodeling.
Title: CYLD Deubiquitinates Nicotinamide Adenine Dinucleotide Phosphate Oxidase 4 Contributing to Adventitial Remodeling.
CYLD interrupts the ERK- and p38-/AP-1 and c-Myc pathways to suppress Nrf2-operated antioxidative capacity, thereby enhancing oxidative stress in the heart.
Title: Deubiquitinating enzyme CYLD mediates pressure overload-induced cardiac maladaptive remodeling and dysfunction via downregulating Nrf2.
Altogether, the results suggest that in the absence of excitatory conditions, constitutive IKK activity at the PSD regulates CYLD and maintains basal levels of K63-linkage specific deubiquitination at the synapse.
Title: IKK regulates the deubiquitinase CYLD at the postsynaptic density.
this study investigates the presence of CYLD at postsynaptic density by immunoblotting and immunoEM, and test whether there are changes in PSD-associated CYLD levels following synaptic activity.
Title: CYLD, a deubiquitinase specific for lysine63-linked polyubiquitins, accumulates at the postsynaptic density in an activity-dependent manner.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables K48-linked deubiquitinase activity	ISO Inferred from Sequence Orthology more info
enables K63-linked deubiquitinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables K63-linked deubiquitinase activity	ISO Inferred from Sequence Orthology more info
enables K63-linked deubiquitinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables Met1-linked polyubiquitin deubiquitinase activity	ISO Inferred from Sequence Orthology 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
enables cysteine-type deubiquitinase activity	ISO Inferred from Sequence Orthology more info
enables cysteine-type deubiquitinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables proline-rich region binding	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables structural constituent of ribosome	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within CD4-positive or CD8-positive, alpha-beta T cell lineage commitment	ISO Inferred from Sequence Orthology more info
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within homeostasis of number of cells	ISO Inferred from Sequence Orthology more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	ISO Inferred from Sequence Orthology more info
involved_in innate immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in necroptotic process	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within necroptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of JNK cascade	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of JNK cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of NF-kappaB transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of interleukin-18-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of interleukin-18-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of non-canonical NF-kappaB signal transduction	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of non-canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of p38MAPK cascade	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of p38MAPK cascade	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within positive regulation of T cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of T cell receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of extrinsic apoptotic signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of extrinsic apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of protein localization	ISO Inferred from Sequence Orthology more info
involved_in protein K63-linked deubiquitination	IBA Inferred from Biological aspect of Ancestor more info
involved_in proteolysis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of B cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of cilium assembly	ISO Inferred from Sequence Orthology more info
involved_in regulation of cilium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in regulation of inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of intrinsic apoptotic signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of intrinsic apoptotic signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of microtubule cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in regulation of mitotic cell cycle	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of necroptotic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of tumor necrosis factor-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of tumor necrosis factor-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within ripoptosome assembly involved in necroptotic process	ISO Inferred from Sequence Orthology more info
involved_in translation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in centrosome	ISS Inferred from Sequence or Structural Similarity more info
located_in ciliary basal body	ISO Inferred from Sequence Orthology more info
located_in ciliary basal body	ISS Inferred from Sequence or Structural Similarity more info
located_in ciliary tip	ISO Inferred from Sequence Orthology more info
located_in ciliary tip	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasmic microtubule	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic microtubule	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasmic side of plasma membrane	ISO Inferred from Sequence Orthology more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
part_of cytosolic small ribosomal subunit	IEA Inferred from Electronic Annotation more info
located_in microtubule	IEA Inferred from Electronic Annotation more info
located_in midbody	ISO Inferred from Sequence Orthology more info
located_in midbody	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in spindle	IEA Inferred from Electronic Annotation more info
located_in spindle	ISO Inferred from Sequence Orthology more info
located_in spindle	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: ubiquitin carboxyl-terminal hydrolase CYLD

Names: 40S ribosomal protein S3a-like; cylindromatosis (turban tumor syndrome); deubiquitinating enzyme CYLD; probable ubiquitin carboxyl-terminal hydrolase CYLD; probable ubiquitin carboxyl-terminal hydrolase CYLD-like; retinitis pigmentosa 1 homolog; ubiquitin thioesterase CYLD; ubiquitin thiolesterase CYLD; ubiquitin-specific-processing protease CYLD

NP_001017380.1

EC 3.4.19.12

XP_038953731.1

EC 3.4.19.12

XP_063134154.1

EC 3.4.19.12

XP_063134155.1

EC 3.4.19.12

XP_063134156.1

EC 3.4.19.12

XP_063134157.1

EC 3.4.19.12

XP_063134158.1

EC 3.4.19.12

XP_063134160.1

EC 3.4.19.12

XP_063134161.1

EC 3.4.19.12

XP_063134162.1

EC 3.4.19.12

XP_063134163.1

EC 3.4.19.12

XP_063134164.1

EC 3.4.19.12

XP_063134165.1

EC 3.4.19.12

XP_063134166.1

EC 3.4.19.12

XP_063134167.1

EC 3.4.19.12

XP_063134168.1

EC 3.4.19.12

XP_063134169.1

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_001017380.1 → NP_001017380.1 ubiquitin carboxyl-terminal hydrolase CYLD

See identical proteins and their annotated locations for NP_001017380.1

Status: PROVISIONAL

Source sequence(s)

BC082001

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96, F1LPJ6

Related

ENSRNOP00000080956.1, ENSRNOT00000106199.1

Conserved Domains (4) summary

smart01052
Location:469 → 537

CAP_GLY; Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network

cd02670
Location:590 → 945

Peptidase_C19N; 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 ...

cl02553
Location:825 → 888

Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...

pfam16607
Location:304 → 468

CYLD_phos_site; Phosphorylation region of CYLD, unstructured

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_086037.1 Reference GRCr8

Range

34487491..34547311 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063278097.1 → XP_063134167.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X4
XM_063278096.1 → XP_063134166.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X3
XM_063278098.1 → XP_063134168.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X5
XM_063278095.1 → XP_063134165.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X2
XM_063278092.1 → XP_063134162.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X1

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96
XM_063278086.1 → XP_063134156.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X1

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96
XM_063278093.1 → XP_063134163.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X1

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96
XM_063278087.1 → XP_063134157.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X1

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96
XM_063278091.1 → XP_063134161.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X1

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96
XM_063278094.1 → XP_063134164.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X1

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96
XM_063278085.1 → XP_063134155.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X1

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96
XM_063278099.1 → XP_063134169.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X6
XM_063278084.1 → XP_063134154.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X1

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96
XM_063278088.1 → XP_063134158.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X1

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96
XM_063278090.1 → XP_063134160.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X1

UniProtKB/Swiss-Prot

Q66H62

UniProtKB/TrEMBL

A6KD96
XM_039097803.2 → XP_038953731.1 ubiquitin carboxyl-terminal hydrolase CYLD isoform X7

Conserved Domains (2) summary

cd02670
Location:268 → 623

Peptidase_C19N; 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 ...

pfam01015
Location:21 → 215

Ribosomal_S3Ae; Ribosomal S3Ae family