Rpf1 (ribosome production factor 1) - Rat Genome Database

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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 located in nucleus. 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
Black 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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2238,063,295 - 238,078,838 (-)EnsemblGRCr8
mRatBN7.22235,403,020 - 235,417,546 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2235,403,021 - 235,417,807 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2243,198,763 - 243,213,280 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02241,090,167 - 241,104,706 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02235,956,400 - 235,970,917 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02252,368,316 - 252,382,838 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2252,368,329 - 252,382,955 (-)Ensemblrn6Rnor6.0
Rnor_5.02270,895,281 - 270,909,803 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42244,711,216 - 244,725,738 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2227,382,731 - 227,397,253 (-)NCBICelera
Cytogenetic Map2q44NCBI
JBrowse:




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 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2238,063,295 - 238,078,838 (-)EnsemblGRCr8
mRatBN7.22235,403,020 - 235,417,546 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2235,403,021 - 235,417,807 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2243,198,763 - 243,213,280 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02241,090,167 - 241,104,706 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02235,956,400 - 235,970,917 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02252,368,316 - 252,382,838 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2252,368,329 - 252,382,955 (-)Ensemblrn6Rnor6.0
Rnor_5.02270,895,281 - 270,909,803 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42244,711,216 - 244,725,738 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
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 Ensembl184,479,257 - 84,498,352 (+)Ensemblhg38GRCh38
GRCh37184,944,949 - 84,964,035 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36184,717,508 - 84,736,621 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm383146,506,344 - 146,521,423 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3146,505,956 - 146,521,429 (-)Ensemblmm10GRCm38
MGSCv373146,169,308 - 146,184,387 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha666,046,093 - 66,067,574 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0663,937,676 - 63,959,213 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (-)EnsemblsusScr11Sscrofa11.1
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474212,972,948 - 12,994,605 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Rpf1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1314,382,159 - 14,396,927 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rpf1
98 total Variants
miRNA Target Status (No longer updated)

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
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2170656145239614549Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2221088977243501206Rat
631501Bp101Blood pressure QTL 1012.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2205135267250135267Rat
2307174Activ3Activity QTL 34.830.000058locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)2210956252251712708Rat
8693697Alc36Alcohol consumption QTL 3620.592drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2219814164239320906Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2143344967251712708Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2214404877251712708Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2143344967251712708Rat
2293833Kiddil8Kidney dilation QTL 82.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2220274283249795005Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2203664411248664411Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2204795005249795005Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2214404877251712708Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2214404877251712708Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2218051934251712708Rat
8693622Alc26Alcohol consumption QTL 262.40.667drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2223810546243965570Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2214404877251712708Rat
2293844Kiddil7Kidney dilation QTL 73.5kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)2220274283249795005Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2151869660251712708Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2196140964251540988Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2205135267250135267Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2214404877251712708Rat
70175BpQTLCluster3Blood pressure QTL cluster 34.128arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)2205135267250135267Rat

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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000021705   ⟹   ENSRNOP00000021705
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2238,063,295 - 238,078,838 (-)Ensembl
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
GRCr8 Ensembl2238,063,337 - 238,078,838 (-)Ensembl
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:
Protein Sequences
Protein RefSeqs NP_001094264 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH86515 (Get FASTA)   NCBI Sequence Viewer  
  AAI66888 (Get FASTA)   NCBI Sequence Viewer  
  AAI66920 (Get FASTA)   NCBI Sequence Viewer  
  EDL82426 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000021705
  ENSRNOP00000077854.1
GenBank Protein Q5RJS9 (Get FASTA)   NCBI Sequence Viewer  
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, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000021705 ENTREZGENE
  ENSRNOT00000100500.1 UniProtKB/Swiss-Prot
Gene3D-CATH Probable brix-domain ribosomal biogenesis protein UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6891440 IMAGE-MGC_LOAD
  IMAGE:6919256 IMAGE-MGC_LOAD
  IMAGE:7301902 IMAGE-MGC_LOAD
InterPro Brix UniProtKB/Swiss-Prot
  IMP4/RPF1 UniProtKB/Swiss-Prot
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
  RIBOSOME PRODUCTION FACTOR 1 UniProtKB/Swiss-Prot
Pfam Brix UniProtKB/Swiss-Prot
PhenoGen Rpf1 PhenoGen
PROSITE BRIX UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000015969 RatGTEx
SMART Brix UniProtKB/Swiss-Prot
Superfamily-SCOP Class II aaRS ABD-related UniProtKB/Swiss-Prot
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