Ybey (ybeY metalloendoribonuclease) - Rat Genome Database

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Gene: Ybey (ybeY metalloendoribonuclease) Rattus norvegicus
Analyze
Symbol: Ybey
Name: ybeY metalloendoribonuclease
RGD ID: 1308722
Description: Predicted to enable RNA endonuclease activity. Predicted to be involved in rRNA processing. Predicted to be located in nucleus. Orthologous to human YBEY (ybeY metalloendoribonuclease); INTERACTS WITH 4,4'-sulfonyldiphenol; alpha-Zearalanol; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: endoribonuclease YbeY; hypothetical protein LOC361822; LOC361822; putative ribonuclease; RGD1308722; rRNA maturation factor homolog; similar to RIKEN cDNA A130042E20, open reading frame 57; ybeY metallopeptidase
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82012,164,678 - 12,175,150 (+)NCBIGRCr8
mRatBN7.22012,165,192 - 12,174,713 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2012,165,237 - 12,174,713 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2012,860,741 - 12,870,241 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02012,221,664 - 12,231,164 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02012,693,443 - 12,702,943 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02012,917,111 - 12,926,587 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2012,917,111 - 12,926,587 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02015,075,086 - 15,084,562 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,580,868 - 12,590,344 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12012,581,121 - 12,587,676 (+)NCBI
Celera2013,663,079 - 13,672,555 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18614015   PMID:22042635   PMID:28153719  


Genomics

Comparative Map Data
Ybey
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82012,164,678 - 12,175,150 (+)NCBIGRCr8
mRatBN7.22012,165,192 - 12,174,713 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2012,165,237 - 12,174,713 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2012,860,741 - 12,870,241 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02012,221,664 - 12,231,164 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02012,693,443 - 12,702,943 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02012,917,111 - 12,926,587 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2012,917,111 - 12,926,587 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02015,075,086 - 15,084,562 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,580,868 - 12,590,344 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12012,581,121 - 12,587,676 (+)NCBI
Celera2013,663,079 - 13,672,555 (+)NCBICelera
Cytogenetic Map20p12NCBI
YBEY
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382146,286,342 - 46,313,225 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2146,286,342 - 46,297,751 (+)EnsemblGRCh38hg38GRCh38
GRCh372147,706,256 - 47,717,665 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362146,530,695 - 46,542,093 (+)NCBINCBI36Build 36hg18NCBI36
Build 342146,530,694 - 46,542,092NCBI
Celera2132,818,701 - 32,831,436 (+)NCBICelera
Cytogenetic Map21q22.3NCBI
HuRef2133,089,429 - 33,101,028 (+)NCBIHuRef
CHM1_12147,267,213 - 47,278,409 (+)NCBICHM1_1
T2T-CHM13v2.02144,668,939 - 44,699,780 (+)NCBIT2T-CHM13v2.0
Ybey
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391076,295,401 - 76,304,948 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1076,295,401 - 76,304,948 (-)EnsemblGRCm39 Ensembl
GRCm381076,457,252 - 76,469,114 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1076,459,567 - 76,469,114 (-)EnsemblGRCm38mm10GRCm38
MGSCv371075,922,312 - 75,931,859 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361075,903,285 - 75,912,830 (-)NCBIMGSCv36mm8
Celera1077,503,956 - 77,513,503 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1038.85NCBI
Ybey
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540742,706,439 - 42,710,962 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540742,706,407 - 42,710,962 (+)NCBIChiLan1.0ChiLan1.0
YBEY
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22242,384,930 - 42,395,508 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12137,257,967 - 37,268,543 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02132,628,599 - 32,638,914 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12145,879,517 - 45,888,717 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2145,879,824 - 45,888,717 (+)Ensemblpanpan1.1panPan2
YBEY
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13139,559,933 - 39,565,775 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3139,561,849 - 39,565,074 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3138,787,728 - 38,793,011 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03139,201,091 - 39,206,441 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.13139,062,760 - 39,068,049 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03139,023,021 - 39,028,763 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03139,541,465 - 39,546,868 (+)NCBIUU_Cfam_GSD_1.0
Ybey
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497138,857,101 - 38,873,809 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936778266,151 - 272,955 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936778265,855 - 273,053 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
YBEY
(Sus scrofa - pig)		 No map positions available.
YBEY
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1289,905,119 - 89,910,307 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl289,905,127 - 89,909,324 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605418,291,574 - 18,300,470 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ybey
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474531,376,747 - 31,382,011 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474531,376,060 - 31,396,319 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ybey
57 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:780
Count of miRNA genes:286
Interacting mature miRNAs:380
Transcripts:ENSRNOT00000038953
Prediction methods:Microtar, Miranda, 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
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20362165614101050Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20460660717617956Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20460660717617956Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20669170617489458Rat
1581577Pur15Proteinuria QTL 154.380.0002urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20804241017617956Rat
4889870Pur30Proteinuria QTL 30190.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20804241029322208Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20903971913461775Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat

Markers in Region
BF398822  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22012,171,192 - 12,171,374 (+)MAPPERmRatBN7.2
Rnor_6.02012,923,067 - 12,923,248NCBIRnor6.0
Rnor_5.02015,081,042 - 15,081,223UniSTSRnor5.0
RGSC_v3.42012,586,824 - 12,587,005UniSTSRGSC3.4
Celera2013,669,035 - 13,669,216UniSTS
RH 3.4 Map20176.57UniSTS
Cytogenetic Map20p12UniSTS
AW530645  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22012,165,383 - 12,165,566 (+)MAPPERmRatBN7.2
Rnor_6.02012,917,258 - 12,917,440NCBIRnor6.0
Rnor_5.02015,075,233 - 15,075,415UniSTSRnor5.0
RGSC_v3.42012,581,015 - 12,581,197UniSTSRGSC3.4
Celera2013,663,226 - 13,663,408UniSTS
RH 3.4 Map20154.94UniSTS
Cytogenetic Map20p12UniSTS
ORF66  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22012,165,702 - 12,167,189 (+)MAPPERmRatBN7.2
Rnor_6.02012,917,577 - 12,919,063NCBIRnor6.0
Rnor_5.02015,075,552 - 15,077,038UniSTSRnor5.0
RGSC_v3.42012,581,334 - 12,582,820UniSTSRGSC3.4
Celera2013,663,545 - 13,665,031UniSTS
Cytogenetic Map20p12UniSTS


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 1 2 6
Low 3 43 56 41 18 41 8 11 74 35 39 5 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000038953   ⟹   ENSRNOP00000030496
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2012,165,237 - 12,174,713 (+)Ensembl
Rnor_6.0 Ensembl2012,917,111 - 12,926,587 (+)Ensembl
RefSeq Acc Id: NM_001108529   ⟹   NP_001101999
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82012,164,723 - 12,174,199 (+)NCBI
mRatBN7.22012,165,237 - 12,174,713 (+)NCBI
Rnor_6.02012,917,111 - 12,926,587 (+)NCBI
Rnor_5.02015,075,086 - 15,084,562 (+)NCBI
RGSC_v3.42012,580,868 - 12,590,344 (+)RGD
Celera2013,663,079 - 13,672,555 (+)RGD
Sequence:
RefSeq Acc Id: XM_006256301   ⟹   XP_006256363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82012,164,678 - 12,170,940 (+)NCBI
mRatBN7.22012,165,192 - 12,174,588 (+)NCBI
Rnor_6.02012,917,112 - 12,924,537 (+)NCBI
Rnor_5.02015,075,086 - 15,084,562 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063279233   ⟹   XP_063135303
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82012,164,678 - 12,175,150 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001101999 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256363 (Get FASTA)   NCBI Sequence Viewer  
  XP_063135303 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97147 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000030496
  ENSRNOP00000030496.4
Reference Protein Sequences
RefSeq Acc Id: NP_001101999   ⟸   NM_001108529
- UniProtKB: D4A815 (UniProtKB/TrEMBL),   A6JKD1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256363   ⟸   XM_006256301
- Peptide Label: isoform X1
- UniProtKB: D4A815 (UniProtKB/TrEMBL),   A6JKD1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030496   ⟸   ENSRNOT00000038953
RefSeq Acc Id: XP_063135303   ⟸   XM_063279233
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A815-F1-model_v2 AlphaFold D4A815 1-164 view protein structure

Transcriptome

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

Promoters
RGD ID:13701518
Promoter ID:EPDNEW_R12042
Type:initiation region
Name:Ybey_1
Description:ybeY metallopeptidase
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_6.02012,917,152 - 12,917,212EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308722 AgrOrtholog
BioCyc Gene G2FUF-4189 BioCyc
Ensembl Genes ENSRNOG00000021365 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000038953 ENTREZGENE
  ENSRNOT00000038953.5 UniProtKB/TrEMBL
Gene3D-CATH 3.40.390.30 UniProtKB/TrEMBL
InterPro MetalPrtase_cat_dom_prd UniProtKB/TrEMBL
  UPF0054 UniProtKB/TrEMBL
  UPF0054_CS UniProtKB/TrEMBL
KEGG Report rno:361822 UniProtKB/TrEMBL
NCBI Gene 361822 ENTREZGENE
PANTHER ENDORIBONUCLEASE YBEY, CHLOROPLASTIC UniProtKB/TrEMBL
  ENDORIBONUCLEASE YBEY, CHLOROPLASTIC UniProtKB/TrEMBL
Pfam UPF0054 UniProtKB/TrEMBL
PhenoGen Ybey PhenoGen
PROSITE UPF0054 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000021365 RatGTEx
Superfamily-SCOP Metalloproteases ('zincins'), catalytic domain UniProtKB/TrEMBL
UniProt A6JKD1 ENTREZGENE, UniProtKB/TrEMBL
  D4A815 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-05-18 Ybey  ybeY metalloendoribonuclease  Ybey  ybeY metallopeptidase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-05-26 Ybey  ybeY metallopeptidase  RGD1308722  similar to RIKEN cDNA A130042E20; open reading frame 57  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1308722  similar to RIKEN cDNA A130042E20; open reading frame 57   RGD1308722_predicted  similar to RIKEN cDNA A130042E20; open reading frame 57 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1308722_predicted  similar to RIKEN cDNA A130042E20; open reading frame 57 (predicted)  LOC361822_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361822_predicted  similar to RIKEN cDNA A130042E20; open reading frame 57 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL