Cyld (CYLD lysine 63 deubiquitinase) - Rat Genome Database

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Gene: Cyld (CYLD lysine 63 deubiquitinase) Rattus norvegicus
Analyze
Symbol: Cyld
Name: CYLD lysine 63 deubiquitinase
RGD ID: 1308346
Description: 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 regulation of necroptotic process; 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 part of cytosolic small ribosomal subunit. Predicted to be active in cytosol. Predicted to colocalize with cytoplasmic microtubule; cytoplasmic side of plasma membrane; and midbody. Human ortholog(s) of this gene implicated in Brooke-Spiegler syndrome. Orthologous to human CYLD (CYLD lysine 63 deubiquitinase); PARTICIPATES IN nuclear factor kappa B signaling pathway; tumor necrosis factor mediated signaling pathway; Retinoic acid-inducible gene (RIG) I-like receptor signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 40S ribosomal protein S3a-like; cylindromatosis (turban tumor syndrome); deubiquitinating enzyme CYLD; LOC100362727; LOC100911739; LOC312937; LRRGT00003; probable ubiquitin carboxyl-terminal hydrolase CYLD; probable ubiquitin carboxyl-terminal hydrolase CYLD-like; retinitis pigmentosa 1 (autosomal dominant); retinitis pigmentosa 1 homolog; retinitis pigmentosa 1 homolog (human); Rp1; Rp1h; ubiquitin carboxyl-terminal hydrolase CYLD; ubiquitin thioesterase CYLD; ubiquitin thiolesterase CYLD; ubiquitin-specific-processing protease CYLD
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Cyld-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81934,487,491 - 34,547,311 (-)NCBIGRCr8
mRatBN7.21918,310,632 - 18,373,696 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1918,314,019 - 18,373,658 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1919,994,711 - 20,053,224 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01925,189,306 - 25,247,825 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01928,146,665 - 28,205,606 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01919,264,984 - 19,323,817 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1919,265,164 - 19,315,357 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01930,298,220 - 30,357,107 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41919,616,209 - 19,619,221 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1918,203,184 - 18,261,162 (-)NCBICelera
Cytogenetic Map19p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (EXP)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
aripiprazole  (ISO)
arsenous acid  (ISO)
atazanavir sulfate  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
butanal  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chenodeoxycholic acid  (ISO)
chlorpyrifos  (ISO)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cylindrospermopsin  (ISO)
cypermethrin  (ISO)
deoxycholic acid  (ISO)
diarsenic trioxide  (ISO)
dicrotophos  (ISO)
dorsomorphin  (ISO)
doxorubicin  (EXP,ISO)
emodin  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (ISO)
fenthion  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
FR900359  (ISO)
furan  (EXP)
gallic acid  (ISO)
gentamycin  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glyphosate  (ISO)
hexadecanoic acid  (EXP)
L-methionine  (ISO)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
methapyrilene  (EXP)
methidathion  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
nefazodone  (ISO)
nickel atom  (ISO)
ozone  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
pirinixic acid  (ISO)
raloxifene  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
Soman  (EXP)
sorafenib  (ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
triclosan  (ISO)
triptonide  (ISO)
tyrphostin AG 1478  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vincristine  (ISO)
vorinostat  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
biological_process  (ND)
CD4-positive or CD8-positive, alpha-beta T cell lineage commitment  (ISO)
cell differentiation  (IEA)
homeostasis of number of cells  (ISO)
innate immune response  (IEA,ISO,ISS)
necroptotic process  (IBA,IEA,ISO)
negative regulation of canonical Wnt signaling pathway  (ISO,ISS)
negative regulation of inflammatory response  (ISO,ISS)
negative regulation of interleukin-18-mediated signaling pathway  (ISO,ISS)
negative regulation of JNK cascade  (ISO,ISS)
negative regulation of non-canonical NF-kappaB signal transduction  (ISO,ISS)
negative regulation of p38MAPK cascade  (ISO,ISS)
positive regulation of extrinsic apoptotic signaling pathway  (IBA,IEA,ISO)
positive regulation of protein localization  (ISO)
positive regulation of T cell differentiation  (ISO)
positive regulation of T cell receptor signaling pathway  (ISO)
proteolysis  (IEA)
regulation of B cell differentiation  (ISO)
regulation of cilium assembly  (ISO,ISS)
regulation of inflammatory response  (ISO,ISS)
regulation of intrinsic apoptotic signaling pathway  (IBA,IEA,ISO)
regulation of microtubule cytoskeleton organization  (ISO)
regulation of mitotic cell cycle  (IBA,IEA,ISO)
regulation of necroptotic process  (ISO)
regulation of neurotransmitter receptor localization to postsynaptic specialization membrane  (IDA,IMP)
regulation of tumor necrosis factor-mediated signaling pathway  (ISO,ISS)
regulation protein catabolic process at postsynapse  (IDA,IEP,IMP)
ripoptosome assembly involved in necroptotic process  (ISO)
translation  (IEA)
Wnt signaling pathway  (IEA)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Identification of the familial cylindromatosis tumour-suppressor gene. Bignell GR, etal., Nat Genet. 2000 Jun;25(2):160-5.
2. Regulation of NF-kappaB by ubiquitination. Chen J and Chen ZJ, Curr Opin Immunol. 2013 Feb;25(1):4-12. doi: 10.1016/j.coi.2012.12.005. Epub 2013 Jan 8.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Deubiquitinases in the regulation of NF-kappaB signaling. Harhaj EW and Dixit VM, Cell Res. 2011 Jan;21(1):22-39. doi: 10.1038/cr.2010.166. Epub 2010 Nov 30.
6. Proteasome-independent polyubiquitin linkage regulates synapse scaffolding, efficacy, and plasticity. Ma Q, etal., Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):E8760-E8769. doi: 10.1073/pnas.1620153114. Epub 2017 Sep 25.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. Comprehensive gene review and curation RGD comprehensive gene curation
15. CaMKII mediates recruitment and activation of the deubiquitinase CYLD at the postsynaptic density. Thein S, etal., PLoS One. 2014 Mar 10;9(3):e91312. doi: 10.1371/journal.pone.0091312. eCollection 2014.
Additional References at PubMed
PMID:12477932   PMID:15341735   PMID:16501569   PMID:17495026   PMID:18174161   PMID:18313383   PMID:18636086   PMID:20194890   PMID:20227366   PMID:21052097   PMID:21525013   PMID:22037414  
PMID:23066153   PMID:23146630   PMID:24928390   PMID:25134987   PMID:25931508   PMID:25935309   PMID:26997266   PMID:27458237   PMID:27545878   PMID:27591049   PMID:28633009   PMID:28701375  
PMID:28751569   PMID:29291351   PMID:34216581   PMID:35435104  


Genomics

Comparative Map Data
Cyld
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81934,487,491 - 34,547,311 (-)NCBIGRCr8
mRatBN7.21918,310,632 - 18,373,696 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1918,314,019 - 18,373,658 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1919,994,711 - 20,053,224 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01925,189,306 - 25,247,825 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01928,146,665 - 28,205,606 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01919,264,984 - 19,323,817 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1919,265,164 - 19,315,357 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01930,298,220 - 30,357,107 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41919,616,209 - 19,619,221 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1918,203,184 - 18,261,162 (-)NCBICelera
Cytogenetic Map19p11NCBI
CYLD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381650,742,086 - 50,801,935 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1650,742,050 - 50,801,935 (+)EnsemblGRCh38hg38GRCh38
GRCh371650,775,997 - 50,835,846 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361649,333,462 - 49,393,347 (+)NCBINCBI36Build 36hg18NCBI36
Build 341649,333,485 - 49,390,029NCBI
Celera1635,291,289 - 35,351,164 (+)NCBICelera
Cytogenetic Map16q12.1NCBI
HuRef1636,663,187 - 36,723,275 (+)NCBIHuRef
CHM1_11652,183,487 - 52,243,322 (+)NCBICHM1_1
T2T-CHM13v2.01656,539,727 - 56,599,616 (+)NCBIT2T-CHM13v2.0
Cyld
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39889,423,506 - 89,478,574 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl889,423,675 - 89,478,573 (+)EnsemblGRCm39 Ensembl
GRCm38888,696,878 - 88,751,946 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl888,697,028 - 88,751,945 (+)EnsemblGRCm38mm10GRCm38
MGSCv37891,220,927 - 91,275,844 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36891,587,180 - 91,638,560 (+)NCBIMGSCv36mm8
Celera892,977,380 - 93,032,328 (+)NCBICelera
Cytogenetic Map8C3NCBI
cM Map843.51NCBI
Cyld
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554338,788,655 - 8,845,925 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554338,788,867 - 8,845,925 (+)NCBIChiLan1.0ChiLan1.0
CYLD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21860,198,381 - 60,258,607 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11666,104,132 - 66,168,240 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01631,004,393 - 31,064,546 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11649,882,751 - 49,942,629 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1649,882,751 - 49,942,629 (+)Ensemblpanpan1.1panPan2
CYLD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1264,561,684 - 64,628,829 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl264,562,503 - 64,628,175 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha261,134,885 - 61,201,742 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0265,106,294 - 65,174,257 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl265,102,752 - 65,174,189 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1261,931,223 - 61,997,967 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0262,949,929 - 63,017,871 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0263,838,510 - 63,905,381 (-)NCBIUU_Cfam_GSD_1.0
Cyld
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934955,773,668 - 55,838,158 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364753,750,882 - 3,812,118 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364753,750,917 - 3,812,118 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CYLD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl634,059,081 - 34,121,264 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1634,058,091 - 34,121,939 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2630,402,013 - 30,416,351 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CYLD
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1536,541,022 - 36,600,874 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl536,541,764 - 36,595,417 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604739,901,441 - 39,961,399 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cyld
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247575,895,912 - 5,953,485 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cyld
181 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:54
Interacting mature miRNAs:60
Transcripts:ENSRNOT00000018888
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032318023069265Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191392640130303727Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191511459834521833Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 15 19 64 16 35 11
Low 2 43 42 41 41 8 11 10 19 6 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001017380 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039097803 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278084 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278085 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278087 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278090 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278091 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278092 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278093 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278094 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278096 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278098 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063278099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AY383658 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC082001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474037 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000018888   ⟹   ENSRNOP00000018888
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1918,314,019 - 18,373,644 (-)Ensembl
Rnor_6.0 Ensembl1919,265,164 - 19,315,357 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091626   ⟹   ENSRNOP00000070060
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1918,314,019 - 18,337,204 (-)Ensembl
Rnor_6.0 Ensembl1919,265,164 - 19,287,643 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000096013   ⟹   ENSRNOP00000094491
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1918,314,019 - 18,337,204 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103615   ⟹   ENSRNOP00000089810
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1918,314,019 - 18,373,644 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106199   ⟹   ENSRNOP00000080956
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1918,314,934 - 18,373,658 (-)Ensembl
RefSeq Acc Id: NM_001017380   ⟹   NP_001017380
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,488,582 - 34,547,118 (-)NCBI
mRatBN7.21918,315,110 - 18,373,650 (-)NCBI
Rnor_6.01919,264,984 - 19,323,817 (-)NCBI
Rnor_5.01930,298,220 - 30,357,107 (-)NCBI
Celera1918,203,184 - 18,261,162 (-)RGD
Sequence:
RefSeq Acc Id: XM_039097803   ⟹   XP_038953731
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,510,569 (-)NCBI
mRatBN7.21918,310,632 - 18,337,160 (-)NCBI
RefSeq Acc Id: XM_063278084   ⟹   XP_063134154
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,546,954 (-)NCBI
RefSeq Acc Id: XM_063278085   ⟹   XP_063134155
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,546,954 (-)NCBI
RefSeq Acc Id: XM_063278086   ⟹   XP_063134156
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,547,129 (-)NCBI
RefSeq Acc Id: XM_063278087   ⟹   XP_063134157
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,547,079 (-)NCBI
RefSeq Acc Id: XM_063278088   ⟹   XP_063134158
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,546,934 (-)NCBI
RefSeq Acc Id: XM_063278090   ⟹   XP_063134160
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,546,921 (-)NCBI
RefSeq Acc Id: XM_063278091   ⟹   XP_063134161
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,546,969 (-)NCBI
RefSeq Acc Id: XM_063278092   ⟹   XP_063134162
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,547,311 (-)NCBI
RefSeq Acc Id: XM_063278093   ⟹   XP_063134163
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,547,092 (-)NCBI
RefSeq Acc Id: XM_063278094   ⟹   XP_063134164
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,546,954 (-)NCBI
RefSeq Acc Id: XM_063278095   ⟹   XP_063134165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,547,311 (-)NCBI
RefSeq Acc Id: XM_063278096   ⟹   XP_063134166
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,547,311 (-)NCBI
RefSeq Acc Id: XM_063278097   ⟹   XP_063134167
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,547,311 (-)NCBI
RefSeq Acc Id: XM_063278098   ⟹   XP_063134168
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,547,311 (-)NCBI
RefSeq Acc Id: XM_063278099   ⟹   XP_063134169
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81934,487,491 - 34,546,954 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001017380   ⟸   NM_001017380
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL),   F1LPJ6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018888   ⟸   ENSRNOT00000018888
RefSeq Acc Id: ENSRNOP00000070060   ⟸   ENSRNOT00000091626
RefSeq Acc Id: XP_038953731   ⟸   XM_039097803
- Peptide Label: isoform X7
RefSeq Acc Id: ENSRNOP00000080956   ⟸   ENSRNOT00000106199
RefSeq Acc Id: ENSRNOP00000094491   ⟸   ENSRNOT00000096013
RefSeq Acc Id: ENSRNOP00000089810   ⟸   ENSRNOT00000103615
RefSeq Acc Id: XP_063134167   ⟸   XM_063278097
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063134166   ⟸   XM_063278096
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063134168   ⟸   XM_063278098
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063134165   ⟸   XM_063278095
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063134162   ⟸   XM_063278092
- Peptide Label: isoform X1
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134156   ⟸   XM_063278086
- Peptide Label: isoform X1
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134163   ⟸   XM_063278093
- Peptide Label: isoform X1
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134157   ⟸   XM_063278087
- Peptide Label: isoform X1
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134161   ⟸   XM_063278091
- Peptide Label: isoform X1
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134164   ⟸   XM_063278094
- Peptide Label: isoform X1
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134155   ⟸   XM_063278085
- Peptide Label: isoform X1
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134169   ⟸   XM_063278099
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063134154   ⟸   XM_063278084
- Peptide Label: isoform X1
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134158   ⟸   XM_063278088
- Peptide Label: isoform X1
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063134160   ⟸   XM_063278090
- Peptide Label: isoform X1
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot),   A6KD96 (UniProtKB/TrEMBL)
Protein Domains
CAP-Gly   USP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q66H62-F1-model_v2 AlphaFold Q66H62 1-953 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700980
Promoter ID:EPDNEW_R11498
Type:initiation region
Name:Cyld_1
Description:CYLD lysine 63 deubiquitinase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01919,287,681 - 19,287,741EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308346 AgrOrtholog
BioCyc Gene G2FUF-6285 BioCyc
Ensembl Genes ENSRNOG00000014048 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018888.8 UniProtKB/TrEMBL
  ENSRNOT00000091626.2 UniProtKB/TrEMBL
  ENSRNOT00000096013.1 UniProtKB/TrEMBL
  ENSRNOT00000103615.1 UniProtKB/TrEMBL
  ENSRNOT00000106199 ENTREZGENE
  ENSRNOT00000106199.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.190 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cysteine proteinases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CAP-Gly_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CAP-Gly_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Papain-like_cys_pep_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peptidase_C19_UCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ribosomal_S1/3_euk UniProtKB/TrEMBL
  Ribosomal_S3Ae UniProtKB/TrEMBL
  USP_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  USP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:312937 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 312937 ENTREZGENE
PANTHER 40S RIBOSOMAL PROTEIN S3A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  40S RIBOSOMAL PROTEIN S3A UniProtKB/TrEMBL
  UBIQUITIN CARBOXYL-TERMINAL HYDROLASE CYLD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam CAP_GLY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CYLD_phos_site UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ribosomal_S3Ae UniProtKB/TrEMBL
  UCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cyld PhenoGen
PROSITE CAP_GLY_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CAP_GLY_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  USP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  USP_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000014048 RatGTEx
SMART CAP_GLY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ribosomal_S3Ae UniProtKB/TrEMBL
Superfamily-SCOP SSF54001 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF74924 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZS00_RAT UniProtKB/TrEMBL
  A0A8I6AAK9_RAT UniProtKB/TrEMBL
  A0A8I6AHV9_RAT UniProtKB/TrEMBL
  A6KD96 ENTREZGENE, UniProtKB/TrEMBL
  CYLD_RAT UniProtKB/Swiss-Prot
  F1LPJ6 ENTREZGENE, UniProtKB/TrEMBL
  Q66H62 ENTREZGENE
  Q6TXJ6_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Cyld  CYLD lysine 63 deubiquitinase  LOC100911739  40S ribosomal protein S3a-like  Data merged from RGD:6490778 737654 PROVISIONAL
2016-02-24 Cyld  CYLD lysine 63 deubiquitinase  Cyld  cylindromatosis (turban tumor syndrome)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-29 Cyld  cylindromatosis (turban tumor syndrome)  LOC100362727  ubiquitin carboxyl-terminal hydrolase CYLD  Data merged from RGD:2324131 737654 PROVISIONAL
2013-05-24 Cyld  cylindromatosis (turban tumor syndrome)  LOC100360670  probable ubiquitin carboxyl-terminal hydrolase CYLD-like  Data merged from RGD:2321687 1643240 APPROVED
2012-07-05 LOC100911739  40S ribosomal protein S3a-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-06 LOC100360670  probable ubiquitin carboxyl-terminal hydrolase CYLD-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-06 LOC100362727  ubiquitin carboxyl-terminal hydrolase CYLD      Symbol and Name status set to provisional 70820 PROVISIONAL
2007-04-04 Cyld  cylindromatosis (turban tumor syndrome)  Rp1h  retinitis pigmentosa 1 homolog (human)  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2006-03-30 Rp1h  retinitis pigmentosa 1 homolog (human)  Rp1  retinitis pigmentosa 1 (autosomal dominant)  Symbol and Name updated 1299863 APPROVED
2005-12-06 Rp1  retinitis pigmentosa 1 (autosomal dominant)  Rp1_predicted  retinitis pigmentosa 1 (autosomal dominant) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Rp1_predicted  retinitis pigmentosa 1 (autosomal dominant) (predicted)      Symbol and Name status set to approved 70820 APPROVED