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 have several functions, including proline-rich region binding activity; ubiquitinyl hydrolase activity; and zinc ion binding activity. Predicted to be involved in several processes, including protein deubiquitination; regulation of lymphocyte differentiation; and regulation of signal transduction. Predicted to colocalize with cytoplasmic microtubule and midbody. Human ortholog(s) of this gene implicated in Brooke-Spiegler syndrome and amyotrophic lateral sclerosis. 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; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also 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: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21918,310,632 - 18,373,696 (-)NCBI
Rnor_6.0 Ensembl1919,265,164 - 19,315,357 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01919,264,984 - 19,323,817 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01930,298,220 - 30,357,107 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41919,616,209 - 19,619,221 (-)NCBIRGSC3.4rn4RGSC3.4
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
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
antirheumatic drug  (ISO)
aripiprazole  (ISO)
arsenous acid  (ISO)
atazanavir sulfate  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
butanal  (ISO)
carbon nanotube  (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  (ISO)
emodin  (ISO)
ethanol  (ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
glycochenodeoxycholic acid  (ISO)
glycocholic acid  (ISO)
glycodeoxycholic acid  (ISO)
glyphosate  (ISO)
L-methionine  (ISO)
leflunomide  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
methylseleninic acid  (ISO)
nefazodone  (ISO)
nickel atom  (ISO)
ozone  (ISO)
paracetamol  (ISO)
pentanal  (ISO)
pirinixic acid  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
Soman  (EXP)
sorafenib  (ISO)
tetraphene  (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,ISO)
negative regulation of canonical Wnt signaling pathway  (IEA,ISO,ISS)
negative regulation of JNK cascade  (IEA,ISO,ISS)
negative regulation of NF-kappaB transcription factor activity  (IBA,IEA,ISO,ISS)
negative regulation of NIK/NF-kappaB signaling  (IEA,ISO,ISS)
negative regulation of p38MAPK cascade  (IEA,ISO,ISS)
negative regulation of T cell differentiation  (ISO)
positive regulation of cellular protein localization  (ISO)
positive regulation of extrinsic apoptotic signaling pathway  (IBA,IEA,ISO)
positive regulation of T cell differentiation  (ISO)
positive regulation of T cell receptor signaling pathway  (ISO)
protein deubiquitination  (ISO,ISS)
protein K48-linked deubiquitination  (IEA)
protein K63-linked deubiquitination  (IBA,IEA,ISO,ISS)
protein linear deubiquitination  (IEA,ISO,ISS)
regulation of B cell differentiation  (ISO)
regulation of cilium assembly  (ISO,ISS)
regulation of inflammatory response  (IEA,ISO,ISS)
regulation of intrinsic apoptotic signaling pathway  (IBA,IEA,ISO)
regulation of microtubule cytoskeleton organization  (IEA,ISO)
regulation of mitotic cell cycle  (IBA,IEA,ISO)
regulation of necroptotic process  (IEA,ISO)
regulation of protein binding  (ISO)
regulation of tumor necrosis factor-mediated signaling pathway  (IEA,ISO,ISS)
ripoptosome assembly involved in necroptotic process  (ISO)
translation  (IEA)
ubiquitin-dependent protein catabolic process  (IEA)
Wnt signaling pathway  (IEA)

Cellular Component

Molecular Function

References

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  


Genomics

Comparative Map Data
Cyld
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21918,310,632 - 18,373,696 (-)NCBI
Rnor_6.0 Ensembl1919,265,164 - 19,315,357 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01919,264,984 - 19,323,817 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01930,298,220 - 30,357,107 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41919,616,209 - 19,619,221 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1918,203,184 - 18,261,162 (-)NCBICelera
Cytogenetic Map19p11NCBI
CYLD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1650,742,050 - 50,801,935 (+)EnsemblGRCh38hg38GRCh38
GRCh381650,742,086 - 50,801,935 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371650,775,997 - 50,835,846 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361649,333,462 - 49,393,347 (+)NCBINCBI36hg18NCBI36
Build 341649,333,485 - 49,390,029NCBI
Celera1635,291,289 - 35,351,164 (+)NCBI
Cytogenetic Map16q12.1NCBI
HuRef1636,663,187 - 36,723,275 (+)NCBIHuRef
CHM1_11652,183,487 - 52,243,322 (+)NCBICHM1_1
Cyld
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39889,423,506 - 89,478,574 (+)NCBIGRCm39mm39
GRCm39 Ensembl889,423,656 - 89,478,573 (+)Ensembl
GRCm38888,696,878 - 88,751,946 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl888,697,028 - 88,751,945 (+)EnsemblGRCm38mm10GRCm38
MGSCv37891,220,927 - 91,275,844 (+)NCBIGRCm37mm9NCBIm37
MGSCv36891,587,180 - 91,638,560 (+)NCBImm8
Celera892,977,380 - 93,032,328 (+)NCBICelera
Cytogenetic Map8C3NCBI
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
PanPan1.11649,882,751 - 49,942,629 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1649,882,751 - 49,942,629 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01631,004,393 - 31,064,546 (+)NCBIMhudiblu_PPA_v0panPan3
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 (-)NCBI
ROS_Cfam_1.0265,106,294 - 65,174,257 (-)NCBI
UMICH_Zoey_3.1261,931,223 - 61,997,967 (-)NCBI
UNSW_CanFamBas_1.0262,949,929 - 63,017,871 (-)NCBI
UU_Cfam_GSD_1.0263,838,510 - 63,905,381 (-)NCBI
Cyld
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934955,773,668 - 55,838,158 (-)NCBI
SpeTri2.0NW_0049364753,750,917 - 3,812,118 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CYLD
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl634,059,941 - 34,121,272 (-)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1536,541,022 - 36,600,874 (+)NCBI
ChlSab1.1 Ensembl536,541,764 - 36,595,417 (+)Ensembl
Vero_WHO_p1.0NW_02366604739,901,441 - 39,961,399 (-)NCBI
Cyld
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247575,895,912 - 5,953,485 (-)NCBI


QTLs in Region (Rnor_6.0)
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)19124933090Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127635288Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19129558305Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19129558305Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19132379055Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19138221845Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19138221845Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19138221845Rat
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)19138221845Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19104464846044648Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19195770746957707Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19243296347217667Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)19370183548701835Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)19370183548701835Rat
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)19500757143907843Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19807254547318201Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191073992926201726Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191130392747879277Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191529452433991703Rat
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)191593952838798459Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191702800352538299Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat

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.


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018888   ⟹   ENSRNOP00000018888
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1919,265,164 - 19,315,357 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091626   ⟹   ENSRNOP00000070060
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1919,265,164 - 19,287,643 (-)Ensembl
RefSeq Acc Id: NM_001017380   ⟹   NP_001017380
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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_039097796   ⟹   XP_038953724
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,310,632 - 18,373,696 (-)NCBI
RefSeq Acc Id: XM_039097797   ⟹   XP_038953725
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,310,632 - 18,373,696 (-)NCBI
RefSeq Acc Id: XM_039097798   ⟹   XP_038953726
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,310,632 - 18,373,696 (-)NCBI
RefSeq Acc Id: XM_039097799   ⟹   XP_038953727
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,310,632 - 18,373,696 (-)NCBI
RefSeq Acc Id: XM_039097800   ⟹   XP_038953728
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,310,632 - 18,373,696 (-)NCBI
RefSeq Acc Id: XM_039097801   ⟹   XP_038953729
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,310,632 - 18,373,696 (-)NCBI
RefSeq Acc Id: XM_039097802   ⟹   XP_038953730
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,310,632 - 18,373,696 (-)NCBI
RefSeq Acc Id: XM_039097803   ⟹   XP_038953731
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21918,310,632 - 18,337,160 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001017380   ⟸   NM_001017380
- UniProtKB: Q66H62 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018888   ⟸   ENSRNOT00000018888
RefSeq Acc Id: ENSRNOP00000070060   ⟸   ENSRNOT00000091626
RefSeq Acc Id: XP_038953730   ⟸   XM_039097802
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038953727   ⟸   XM_039097799
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038953726   ⟸   XM_039097798
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038953729   ⟸   XM_039097801
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038953728   ⟸   XM_039097800
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038953725   ⟸   XM_039097797
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038953724   ⟸   XM_039097796
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038953731   ⟸   XM_039097803
- Peptide Label: isoform X8
Protein Domains
CAP-Gly   USP

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308346 AgrOrtholog
Ensembl Genes ENSRNOG00000014048 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018888 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000070060 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018888 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000091626 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.190 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
NCBI Gene 312937 ENTREZGENE
Pfam CAP_GLY 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
  CAP_GLY_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  USP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  USP_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 CYLD_RAT UniProtKB/Swiss-Prot
  F1LPJ6_RAT 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 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 737654 PROVISIONAL
2013-05-24 Cyld  cylindromatosis (turban tumor syndrome)  LOC100360670  probable ubiquitin carboxyl-terminal hydrolase CYLD-like  Data Merged 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