Rrp1b (ribosomal RNA processing 1B) - Rat Genome Database

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Gene: Rrp1b (ribosomal RNA processing 1B) Rattus norvegicus
Analyze
Symbol: Rrp1b
Name: ribosomal RNA processing 1B
RGD ID: 1305633
Description: Predicted to enable transcription coactivator activity. Predicted to be involved in several processes, including negative regulation of GTPase activity; positive regulation by host of viral transcription; and regulation of RNA metabolic process. Predicted to be located in chromatin and nuclear lumen. Predicted to be part of preribosome, large subunit precursor. Predicted to be active in nucleus. Orthologous to human RRP1B (ribosomal RNA processing 1B); INTERACTS WITH acrylamide; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC309673; RGD1305633; ribosomal RNA processing 1 homolog B; ribosomal RNA processing 1 homolog B (S. cerevisiae); ribosomal RNA processing protein 1 homolog B; similar to RIKEN cDNA 2600005C20
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22010,123,111 - 10,148,704 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2010,123,125 - 10,147,928 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.02010,844,234 - 10,869,830 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2010,844,266 - 10,869,821 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02013,016,065 - 13,041,641 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42010,454,161 - 10,478,482 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12010,454,391 - 10,477,785 (+)NCBI
Celera2011,633,485 - 11,659,795 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16780588   PMID:18081427   PMID:19389623   PMID:19710015   PMID:20040599   PMID:20926688   PMID:22658674   PMID:22681889   PMID:23604122   PMID:26311876  


Genomics

Comparative Map Data
Rrp1b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22010,123,111 - 10,148,704 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2010,123,125 - 10,147,928 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.02010,844,234 - 10,869,830 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2010,844,266 - 10,869,821 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02013,016,065 - 13,041,641 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42010,454,161 - 10,478,482 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12010,454,391 - 10,477,785 (+)NCBI
Celera2011,633,485 - 11,659,795 (+)NCBICelera
Cytogenetic Map20p12NCBI
RRP1B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382143,659,560 - 43,696,079 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2143,659,560 - 43,696,079 (+)EnsemblGRCh38hg38GRCh38
GRCh372145,079,441 - 45,115,960 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362143,903,860 - 43,940,388 (+)NCBINCBI36Build 36hg18NCBI36
Build 342143,903,859 - 43,940,386NCBI
Celera2130,185,262 - 30,221,795 (+)NCBICelera
Cytogenetic Map21q22.3NCBI
HuRef2130,447,279 - 30,483,760 (+)NCBIHuRef
CHM1_12144,640,173 - 44,676,715 (+)NCBICHM1_1
T2T-CHM13v2.02142,015,103 - 42,051,622 (+)NCBIT2T-CHM13v2.0
Rrp1b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391732,255,087 - 32,281,839 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1732,255,074 - 32,281,839 (+)EnsemblGRCm39 Ensembl
GRCm381732,036,162 - 32,062,865 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1732,036,100 - 32,062,865 (+)EnsemblGRCm38mm10GRCm38
MGSCv371732,173,107 - 32,199,807 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361731,765,265 - 31,789,709 (+)NCBIMGSCv36mm8
Celera1732,952,734 - 32,979,435 (+)NCBICelera
Cytogenetic Map17B1NCBI
Rrp1b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540738,553,814 - 38,577,465 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540738,553,866 - 38,577,547 (-)NCBIChiLan1.0ChiLan1.0
RRP1B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12143,217,516 - 43,251,192 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2143,217,516 - 43,251,192 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02129,916,109 - 29,952,749 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RRP1B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13137,652,584 - 37,670,396 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3137,652,863 - 37,667,895 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3136,799,783 - 36,824,798 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03137,188,500 - 37,213,308 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3137,188,492 - 37,213,306 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13137,056,330 - 37,081,115 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03137,041,715 - 37,066,909 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03137,534,281 - 37,559,052 (+)NCBIUU_Cfam_GSD_1.0
Rrp1b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497136,867,262 - 36,893,378 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936500575,401 - 601,108 (-)EnsemblSpeTri2.0
SpeTri2.0NW_004936500574,445 - 600,555 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RRP1B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13206,629,204 - 206,651,123 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113206,629,176 - 206,653,374 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213216,628,871 - 216,653,088 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RRP1B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1287,434,214 - 87,471,553 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl287,434,304 - 87,471,627 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605415,500,819 - 15,537,728 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rrp1b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474527,365,141 - 27,387,173 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474527,362,820 - 27,387,258 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rrp1b
171 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:17
Count of miRNA genes:17
Interacting mature miRNAs:17
Transcripts:ENSRNOT00000001583
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 (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

Markers in Region
RH135130  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22010,142,913 - 10,143,110 (+)MAPPERmRatBN7.2
Rnor_6.02010,864,041 - 10,864,237NCBIRnor6.0
Rnor_5.02013,035,852 - 13,036,048UniSTSRnor5.0
RGSC_v3.42010,473,937 - 10,474,133UniSTSRGSC3.4
Celera2011,654,006 - 11,654,202UniSTS
RH 3.4 Map20148.7UniSTS
Cytogenetic Map20p12UniSTS
RH127720  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22010,148,443 - 10,148,624 (+)MAPPERmRatBN7.2
Rnor_6.02010,869,571 - 10,869,751NCBIRnor6.0
Rnor_5.02013,041,382 - 13,041,562UniSTSRnor5.0
RGSC_v3.42010,479,467 - 10,479,647UniSTSRGSC3.4
Celera2011,659,536 - 11,659,716UniSTS
RH 3.4 Map20148.2UniSTS
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 2 26 27 22 8 22 2 61 26 30 3
Low 1 17 30 19 11 19 8 9 13 9 11 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001583   ⟹   ENSRNOP00000001583
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2010,123,125 - 10,147,928 (+)Ensembl
Rnor_6.0 Ensembl2010,844,266 - 10,869,821 (+)Ensembl
RefSeq Acc Id: XM_017601874   ⟹   XP_017457363
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22010,132,206 - 10,148,704 (+)NCBI
Rnor_6.02010,853,334 - 10,869,830 (+)NCBI
Sequence:
RefSeq Acc Id: XM_228076   ⟹   XP_228076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22010,123,111 - 10,148,704 (+)NCBI
Rnor_6.02010,844,234 - 10,869,830 (+)NCBI
Rnor_5.02013,016,065 - 13,041,641 (+)NCBI
RGSC_v3.42010,454,161 - 10,478,482 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_017457363 (Get FASTA)   NCBI Sequence Viewer  
  XP_228076 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97033 (Get FASTA)   NCBI Sequence Viewer  
  EDL97034 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_228076   ⟸   XM_228076
- Peptide Label: isoform X1
- UniProtKB: D3ZY39 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457363   ⟸   XM_017601874
- Peptide Label: isoform X2
- UniProtKB: D3ZY39 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001583   ⟸   ENSRNOT00000001583

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZY39-F1-model_v2 AlphaFold D3ZY39 1-733 view protein structure

Transcriptome

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

Promoters
RGD ID:13701490
Promoter ID:EPDNEW_R12005
Type:multiple initiation site
Name:Rrp1b_1
Description:ribosomal RNA processing 1B
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_6.02010,844,252 - 10,844,312EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305633 AgrOrtholog
BioCyc Gene G2FUF-4288 BioCyc
Ensembl Genes ENSRNOG00000001194 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001583 ENTREZGENE
  ENSRNOP00000001583.7 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001583 ENTREZGENE
  ENSRNOT00000001583.8 UniProtKB/TrEMBL
InterPro Nop52 UniProtKB/TrEMBL
NCBI Gene 309673 ENTREZGENE
PANTHER Nop52 UniProtKB/TrEMBL
Pfam Nop52 UniProtKB/TrEMBL
PhenoGen Rrp1b PhenoGen
UniProt D3ZY39 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-07-12 Rrp1b  ribosomal RNA processing 1B  Rrp1b  ribosomal RNA processing 1 homolog B (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-06 Rrp1b  ribosomal RNA processing 1 homolog B (S. cerevisiae)  RGD1305633_predicted  similar to RIKEN cDNA 2600005C20 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1305633_predicted  similar to RIKEN cDNA 2600005C20 (predicted)  LOC309673_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC309673_predicted  similar to RIKEN cDNA 2600005C20 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL