Rpf1 (ribosome production factor 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Rpf1 (ribosome production factor 1) Rattus norvegicus
Analyze
Symbol: Rpf1
Name: ribosome production factor 1
RGD ID: 1559755
Description: Predicted to enable RNA binding activity. Predicted to be involved in maturation of 5.8S rRNA and maturation of LSU-rRNA. Predicted to be part of preribosome, large subunit precursor. Predicted to be active in nucleolus. Orthologous to human RPF1 (ribosome production factor 1 homolog); INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: brix domain containing 5; brix domain-containing protein 5; Bxdc5; ribosome biogenesis protein RPF1; ribosome production factor 1 homolog; ribosome production factor 1 homolog (S. cerevisiae); RNA processing factor 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82238,063,294 - 238,077,817 (-)NCBIGRCr8
mRatBN7.22235,403,020 - 235,417,546 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2235,403,021 - 235,417,807 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2243,198,763 - 243,213,280 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02241,090,167 - 241,104,706 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02235,956,400 - 235,970,917 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02252,368,316 - 252,382,838 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2252,368,329 - 252,382,955 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02270,895,281 - 270,909,803 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42244,711,216 - 244,725,738 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2227,382,731 - 227,397,253 (-)NCBICelera
Cytogenetic Map2q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:8889548   PMID:11864606   PMID:12429849   PMID:15057822   PMID:15489334   PMID:22681889  


Genomics

Comparative Map Data
Rpf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82238,063,294 - 238,077,817 (-)NCBIGRCr8
mRatBN7.22235,403,020 - 235,417,546 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2235,403,021 - 235,417,807 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2243,198,763 - 243,213,280 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02241,090,167 - 241,104,706 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02235,956,400 - 235,970,917 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02252,368,316 - 252,382,838 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2252,368,329 - 252,382,955 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02270,895,281 - 270,909,803 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42244,711,216 - 244,725,738 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2227,382,731 - 227,397,253 (-)NCBICelera
Cytogenetic Map2q44NCBI
RPF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38184,479,266 - 84,498,352 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl184,479,259 - 84,498,352 (+)EnsemblGRCh38hg38GRCh38
GRCh37184,944,949 - 84,964,035 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36184,717,508 - 84,736,621 (+)NCBINCBI36Build 36hg18NCBI36
Celera183,189,094 - 83,208,206 (+)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef183,055,328 - 83,074,244 (+)NCBIHuRef
CHM1_1185,059,752 - 85,078,863 (+)NCBICHM1_1
T2T-CHM13v2.0184,319,649 - 84,338,734 (+)NCBIT2T-CHM13v2.0
Rpf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393146,212,099 - 146,227,184 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3146,211,711 - 146,227,184 (-)EnsemblGRCm39 Ensembl
GRCm383146,506,344 - 146,521,423 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3146,505,956 - 146,521,429 (-)EnsemblGRCm38mm10GRCm38
MGSCv373146,169,308 - 146,184,387 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363146,443,804 - 146,458,804 (-)NCBIMGSCv36mm8
Celera3152,956,530 - 152,971,609 (-)NCBICelera
Cytogenetic Map3H2NCBI
cM Map371.57NCBI
Rpf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554239,394,780 - 9,412,105 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554239,394,780 - 9,412,001 (-)NCBIChiLan1.0ChiLan1.0
RPF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21142,444,845 - 142,465,459 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11141,599,275 - 141,619,887 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01117,027,638 - 117,046,940 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1185,888,476 - 85,907,539 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl185,888,496 - 85,906,883 (+)Ensemblpanpan1.1panPan2
RPF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1663,399,102 - 63,419,407 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl663,399,102 - 63,419,373 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha666,046,093 - 66,067,574 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0663,937,676 - 63,959,213 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl663,937,682 - 63,959,199 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1663,465,720 - 63,487,197 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0663,434,448 - 63,455,926 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0663,940,417 - 63,961,931 (-)NCBIUU_Cfam_GSD_1.0
Rpf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505895,180,924 - 95,195,592 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366081,110,150 - 1,125,127 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366081,110,100 - 1,125,097 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RPF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6129,256,042 - 129,271,043 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16129,256,040 - 129,271,038 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RPF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12048,855,166 - 48,877,132 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603368,890,876 - 68,909,846 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rpf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474212,969,808 - 12,994,578 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474212,972,948 - 12,994,605 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rpf1
33 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:154
Count of miRNA genes:117
Interacting mature miRNAs:132
Transcripts:ENSRNOT00000021705
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631563Hcuc3Hepatic copper content QTL 33.87liver copper amount (VT:0003065)liver copper weight to liver dry weight ratio (CMO:0001512)2229059610249053267Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2218414747240841241Rat
8693697Alc36Alcohol consumption QTL 3620.592drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2217139753236660713Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2211744537249053267Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2200990457245990457Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2202446871237938339Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2214226044247136170Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2211744537249053267Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2211744537249053267Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2215377404237938339Rat
8693622Alc26Alcohol consumption QTL 262.40.667drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2221136523241305619Rat
7411555Bw132Body weight QTL 1320.001body mass (VT:0001259)body weight gain (CMO:0000420)2223389739249053267Rat
9587428Epfw6Epididymal fat weight QTL 67.470.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)2223389739249053267Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2211744537249053267Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2219753301247136170Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2149559561249053267Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2193452645245889826Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2211744537249053267Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2212828222249053267Rat

Markers in Region
RH132603  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22235,403,613 - 235,403,814 (+)MAPPERmRatBN7.2
Rnor_6.02252,368,910 - 252,369,110NCBIRnor6.0
Rnor_5.02270,895,875 - 270,896,075UniSTSRnor5.0
RGSC_v3.42244,711,810 - 244,712,010UniSTSRGSC3.4
Celera2227,383,325 - 227,383,525UniSTS
Cytogenetic Map2q44UniSTS
BE109298  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2q44UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000021705   ⟹   ENSRNOP00000021705
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2235,403,021 - 235,417,807 (-)Ensembl
Rnor_6.0 Ensembl2252,368,329 - 252,382,955 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100500   ⟹   ENSRNOP00000077854
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2235,403,063 - 235,417,546 (-)Ensembl
RefSeq Acc Id: NM_001100794   ⟹   NP_001094264
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82238,063,294 - 238,077,817 (-)NCBI
mRatBN7.22235,403,020 - 235,417,546 (-)NCBI
Rnor_6.02252,368,316 - 252,382,838 (-)NCBI
Rnor_5.02270,895,281 - 270,909,803 (-)NCBI
RGSC_v3.42244,711,216 - 244,725,738 (-)RGD
Celera2227,382,731 - 227,397,253 (-)RGD
Sequence:
RefSeq Acc Id: NP_001094264   ⟸   NM_001100794
- UniProtKB: B2RYS7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000021705   ⟸   ENSRNOT00000021705
Ensembl Acc Id: ENSRNOP00000077854   ⟸   ENSRNOT00000100500
Protein Domains
Brix

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5RJS9-F1-model_v2 AlphaFold Q5RJS9 1-345 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559755 AgrOrtholog
BioCyc Gene G2FUF-50899 BioCyc
Ensembl Genes ENSRNOG00000015969 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055023440 UniProtKB/Swiss-Prot
  ENSRNOG00060000867 UniProtKB/Swiss-Prot
  ENSRNOG00065012833 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000021705.8 UniProtKB/TrEMBL
  ENSRNOT00000100500.1 UniProtKB/Swiss-Prot
  ENSRNOT00055040278 UniProtKB/Swiss-Prot
  ENSRNOT00060001079 UniProtKB/Swiss-Prot
  ENSRNOT00065020978 UniProtKB/Swiss-Prot
Gene3D-CATH Probable brix-domain ribosomal biogenesis protein UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6891440 IMAGE-MGC_LOAD
  IMAGE:6919256 IMAGE-MGC_LOAD
  IMAGE:7301902 IMAGE-MGC_LOAD
InterPro Brix UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IMP4/RPF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:499725 UniProtKB/TrEMBL
MGC_CLONE MGC:105654 IMAGE-MGC_LOAD
  MGC:188831 IMAGE-MGC_LOAD
  MGC:188908 IMAGE-MGC_LOAD
NCBI Gene 499725 ENTREZGENE
PANTHER PTHR22734 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RIBOSOME PRODUCTION FACTOR 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Brix UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rpf1 PhenoGen
PROSITE BRIX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000015969 RatGTEx
  ENSRNOG00055023440 RatGTEx
  ENSRNOG00060000867 RatGTEx
  ENSRNOG00065012833 RatGTEx
SMART Brix UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Class II aaRS ABD-related UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B2RYS7 ENTREZGENE, UniProtKB/TrEMBL
  F1MA20_RAT UniProtKB/TrEMBL
  Q5RJS9 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-05-05 Rpf1  ribosome production factor 1  Rpf1  ribosome production factor 1 homolog  Name changed 629549 APPROVED
2015-07-30 Rpf1  ribosome production factor 1 homolog  Rpf1  ribosome production factor 1 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-07-29 Rpf1  ribosome production factor 1 homolog (S. cerevisiae)  Bxdc5  brix domain containing 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 Bxdc5  brix domain containing 5      Symbol and Name status set to provisional 70820 PROVISIONAL