Nop53 (NOP53 ribosome biogenesis factor) - Rat Genome Database

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Pathways
Gene: Nop53 (NOP53 ribosome biogenesis factor) Mus musculus
Analyze
Symbol: Nop53
Name: NOP53 ribosome biogenesis factor
RGD ID: 1558540
MGI Page MGI
Description: Predicted to enable 5S rRNA binding activity; identical protein binding activity; and p53 binding activity. Involved in negative regulation of signal transduction by p53 class mediator; positive regulation of proteasomal ubiquitin-dependent protein catabolic process; and protein localization to nucleolus. Located in nucleolus. Is expressed in nucleus pulposus. Orthologous to human NOP53 (NOP53 ribosome biogenesis factor).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 5330430H08Rik; 9430097C02Rik; AU041936; AW536441; glioma tumor suppressor candidate region gene 2; Glts; Gltscr2; PICT-1; R74911; ribosome biogenesis protein NOP53
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Gm6085  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39715,671,760 - 15,680,033 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl715,670,108 - 15,679,999 (-)EnsemblGRCm39 Ensembl
GRCm38715,937,835 - 15,946,108 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl715,936,183 - 15,946,074 (-)EnsemblGRCm38mm10GRCm38
MGSCv37716,523,184 - 16,531,457 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36715,096,357 - 15,104,578 (-)NCBIMGSCv36mm8
Celera713,136,540 - 13,144,813 (-)NCBICelera
Cytogenetic Map7A2NCBI
cM Map78.64NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Mapping of the mouse hyh gene to a YAC/BAC contig on proximal Chromosome 7. Chae TH, etal., Mamm Genome 2002 May;13(5):239-44.
2. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10725249   PMID:10922068   PMID:11042159   PMID:11076861   PMID:12477932   PMID:12520002   PMID:14610273   PMID:14755058   PMID:16141072   PMID:16141073  
PMID:16971513   PMID:17967808   PMID:18799693   PMID:21267068   PMID:21804542   PMID:21873635   PMID:22922362   PMID:34133714  


Genomics

Comparative Map Data
Nop53
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39715,671,760 - 15,680,033 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl715,670,108 - 15,679,999 (-)EnsemblGRCm39 Ensembl
GRCm38715,937,835 - 15,946,108 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl715,936,183 - 15,946,074 (-)EnsemblGRCm38mm10GRCm38
MGSCv37716,523,184 - 16,531,457 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36715,096,357 - 15,104,578 (-)NCBIMGSCv36mm8
Celera713,136,540 - 13,144,813 (-)NCBICelera
Cytogenetic Map7A2NCBI
cM Map78.64NCBI
NOP53
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381947,745,546 - 47,757,058 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1947,745,546 - 47,757,058 (+)EnsemblGRCh38hg38GRCh38
GRCh371948,248,803 - 48,260,315 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361952,940,620 - 52,952,127 (+)NCBINCBI36Build 36hg18NCBI36
Build 341952,940,619 - 52,952,126NCBI
Celera1945,054,495 - 45,066,024 (+)NCBICelera
Cytogenetic Map19q13.33NCBI
HuRef1944,675,424 - 44,686,829 (+)NCBIHuRef
CHM1_11948,251,102 - 48,262,632 (+)NCBICHM1_1
T2T-CHM13v2.01950,576,356 - 50,587,868 (+)NCBIT2T-CHM13v2.0
Nop53
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2176,629,084 - 76,636,902 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl176,629,069 - 76,636,902 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx182,004,061 - 82,011,895 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0190,568,120 - 90,575,954 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0183,759,201 - 83,767,035 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0177,836,522 - 77,843,991 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl177,836,196 - 77,844,189 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0179,101,202 - 79,108,671 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4176,281,104 - 76,288,571 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1176,359,212 - 76,366,682 (-)NCBI
Celera171,119,638 - 71,127,111 (-)NCBICelera
Cytogenetic Map1q21NCBI
Nop53
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555741,506,022 - 1,517,130 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555741,505,997 - 1,514,680 (+)NCBIChiLan1.0ChiLan1.0
NOP53
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11955,768,753 - 55,780,320 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01944,739,739 - 44,751,303 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11953,393,238 - 53,404,708 (+)NCBIpanpan1.1PanPan1.1panPan2
NOP53
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11108,307,039 - 108,315,732 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1108,307,042 - 108,316,495 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1107,789,230 - 107,797,912 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01108,833,077 - 108,841,767 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1108,829,885 - 108,842,457 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11108,501,211 - 108,509,476 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01108,145,336 - 108,154,020 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01109,013,492 - 109,022,181 (-)NCBIUU_Cfam_GSD_1.0
Nop53
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934919,716,350 - 19,725,739 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366641,334,510 - 1,342,321 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366641,334,487 - 1,343,867 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NOP53
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl653,443,385 - 53,452,017 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1653,443,453 - 53,451,707 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2648,973,573 - 48,982,147 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NOP53
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1641,058,199 - 41,070,220 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl641,057,906 - 41,071,202 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607320,811,521 - 20,823,571 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nop53
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248326,145,749 - 6,154,411 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248326,144,260 - 6,154,172 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Nop53
187 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:198
Count of miRNA genes:184
Interacting mature miRNAs:189
Transcripts:ENSMUST00000044158
Prediction methods:Miranda, Rnahybrid
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301177Vent3_mventricular size 3 (mouse)Not determined7120511925Mouse
10054067Sle20_msystematic lupus erythematosus susceptibility 20 (mouse)Not determined7120511925Mouse
1302188Lxw6_mlupus BXSB x NZW 6 (mouse)Not determined7121698146Mouse
12904941Edlmmq6_mextensor digitorum longus muscle mass QTL 6 (mouse)7121821047Mouse
12904948Tammq5_mtibialis anterior muscle mass QTL 5 (mouse)7121821047Mouse
12904953Gmmq5_mgastrocnemius muscle mass QTL 5 (mouse)7121821047Mouse
1301572Sluc30_msusceptibility to lung cancer 30 (mouse)Not determined7243169636431844Mouse
1302115Abhr3_mallergen-induced bronchial hyperresponsiveness 3 (mouse)Not determined7331599616637423Mouse
1301115Lrdm1_mlymphoproliferation (Fas) renal disease modifier 1 (mouse)Not determined7335204824879418Mouse
1300722Sle3_msystemic lupus erythmatosus susceptibility 3 (mouse)Not determined7351172887142720Mouse
38501068Tip1_mtuberculosis immunophenotype 1, spleen CFU (mouse)7360299972549748Mouse
25394569Skmw57_mskeletal muscle weight 57, gastroc (mouse)7458046916687861Mouse
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76502999133501729Mouse
12792978Fbmd3_mfemoral bone mineral density 3, females only (mouse)77050288142367832Mouse
1357699Nhdlq6_mnon-HDL QTL 6 (mouse)Not determined7998886743988984Mouse
1558893Spir1_mStreptococcus pneumoniae infection resistance 1 (mouse)Not determined71030579844305936Mouse
10449139Eosn1_meosinophil differential 1 (mouse)71248087746480877Mouse
10449158Eosn3_meosinophil differential 3 (mouse)71248087746480877Mouse
4141566Femwf8_mfemur work to failure 8 (mouse)Not determined1303248547032621Mouse
11522751Cocia17_mcocaine-induced activity, QTL 17 (mouse)71313520447135204Mouse
25314314Sccor1_msynaptonemal complex length to mean MLH1 count ratio 1 (mouse)71333392547349748Mouse

Markers in Region
AU041936  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38715,938,364 - 15,938,937UniSTSGRCm38
MGSCv37716,523,713 - 16,524,286UniSTSGRCm37
Celera713,137,069 - 13,137,642UniSTS
Cytogenetic Map7A2UniSTS
cM Map715.13UniSTS
Whitehead/MRC_RH1150.55UniSTS
Whitehead/MRC_RH1132.48UniSTS
RH125127  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38715,938,361 - 15,938,937UniSTSGRCm38
MGSCv37716,523,710 - 16,524,286UniSTSGRCm37
Celera713,137,066 - 13,137,642UniSTS
Cytogenetic Map7A2UniSTS
cM Map715.13UniSTS


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_133831 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC148990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI850210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK077341 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK079167 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK088461 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK140286 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK146916 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK151836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK158665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK160070 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK169290 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY535001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC017637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC025810 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BY283382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466654 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSMUST00000044158   ⟹   ENSMUSP00000043981
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl715,670,108 - 15,679,999 (-)Ensembl
GRCm38.p6 Ensembl715,936,183 - 15,946,074 (-)Ensembl
RefSeq Acc Id: ENSMUST00000197477
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl715,671,763 - 15,679,675 (-)Ensembl
GRCm38.p6 Ensembl715,937,838 - 15,945,750 (-)Ensembl
RefSeq Acc Id: ENSMUST00000198688
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl715,671,763 - 15,679,726 (-)Ensembl
GRCm38.p6 Ensembl715,937,838 - 15,945,801 (-)Ensembl
RefSeq Acc Id: ENSMUST00000200455
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl715,676,773 - 15,679,980 (-)Ensembl
GRCm38.p6 Ensembl715,942,848 - 15,946,055 (-)Ensembl
RefSeq Acc Id: NM_133831   ⟹   NP_598592
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39715,671,760 - 15,680,033 (-)NCBI
GRCm38715,937,835 - 15,946,108 (-)ENTREZGENE
MGSCv37716,523,184 - 16,531,457 (-)RGD
Celera713,136,540 - 13,144,813 (-)RGD
cM Map7 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_598592   ⟸   NM_133831
- UniProtKB: Q8VD18 (UniProtKB/Swiss-Prot),   Q8BK35 (UniProtKB/TrEMBL),   Q8BTX4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000043981   ⟸   ENSMUST00000044158

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8BK35-F1-model_v2 AlphaFold Q8BK35 1-484 view protein structure

Promoters
RGD ID:6891894
Promoter ID:EPDNEW_M9398
Type:initiation region
Name:Nop53_1
Description:Mus musculus NOP53 ribosome biogenesis factor , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38715,946,063 - 15,946,123EPDNEW
RGD ID:6841172
Promoter ID:MM_KWN:48870
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:UC009FGQ.1,   UC009FGR.1,   UC009FGS.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36716,531,146 - 16,532,407 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2154441 AgrOrtholog
Ensembl Genes ENSMUSG00000041560 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000044158 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Nop53/GLTSCR2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:68077 UniProtKB/Swiss-Prot
MGD MGI:2154441 ENTREZGENE
NCBI Gene 68077 ENTREZGENE
PANTHER PTHR14211 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RIBOSOME BIOGENESIS PROTEIN NOP53 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Nop53 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nop53 PhenoGen
PIRSF Gltscr2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt NOP53_MOUSE UniProtKB/Swiss-Prot
  Q3USL3_MOUSE UniProtKB/TrEMBL
  Q8BK35 ENTREZGENE
  Q8BTX4 ENTREZGENE, UniProtKB/TrEMBL
  Q8R126_MOUSE UniProtKB/TrEMBL
  Q8VD18 ENTREZGENE
  Q9CV23_MOUSE UniProtKB/TrEMBL
UniProt Secondary Q8VD18 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-04-25 Nop53  NOP53 ribosome biogenesis factor  Gltscr2  glioma tumor suppressor candidate region gene 2  Symbol and/or name change 5135510 APPROVED