Rpusd1 (RNA pseudouridine synthase domain containing 1) - Rat Genome Database

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Gene: Rpusd1 (RNA pseudouridine synthase domain containing 1) Rattus norvegicus
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Symbol: Rpusd1
Name: RNA pseudouridine synthase domain containing 1
RGD ID: 1304934
Description: Predicted to enable RNA binding activity. Orthologous to human RPUSD1 (RNA pseudouridine synthase domain containing 1); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC287148; RGD1304934; RNA pseudouridylate synthase domain containing 1; RNA pseudouridylate synthase domain-containing protein 1; similar to RIKEN cDNA 2310051D06
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
GRCr81015,255,806 - 15,259,730 (+)NCBIGRCr8
mRatBN7.21014,751,310 - 14,755,213 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,751,384 - 14,755,207 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1019,490,309 - 19,494,204 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01018,979,187 - 18,983,081 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01014,479,537 - 14,483,381 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01015,099,104 - 15,102,968 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,099,009 - 15,102,960 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01014,911,797 - 14,915,689 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41014,996,497 - 15,000,351 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11014,996,508 - 15,000,346 (+)NCBI
Celera1014,420,831 - 14,424,687 (+)NCBICelera
Cytogenetic Map10q12NCBI
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

Biological Process

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 MGI mouse gene data--August 2006 MGD 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
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Rpusd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81015,255,806 - 15,259,730 (+)NCBIGRCr8
mRatBN7.21014,751,310 - 14,755,213 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,751,384 - 14,755,207 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1019,490,309 - 19,494,204 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01018,979,187 - 18,983,081 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01014,479,537 - 14,483,381 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01015,099,104 - 15,102,968 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,099,009 - 15,102,960 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01014,911,797 - 14,915,689 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41014,996,497 - 15,000,351 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11014,996,508 - 15,000,346 (+)NCBI
Celera1014,420,831 - 14,424,687 (+)NCBICelera
Cytogenetic Map10q12NCBI
RPUSD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3816784,974 - 788,381 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl16784,974 - 788,397 (-)EnsemblGRCh38hg38GRCh38
GRCh3716834,974 - 838,381 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3616774,975 - 778,384 (-)NCBINCBI36Build 36hg18NCBI36
Build 3416774,975 - 778,384NCBI
Celera161,034,861 - 1,038,270 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef16756,947 - 760,356 (-)NCBIHuRef
CHM1_116834,924 - 838,333 (-)NCBICHM1_1
T2T-CHM13v2.016789,685 - 793,092 (-)NCBIT2T-CHM13v2.0
Rpusd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391725,943,758 - 25,950,438 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1725,946,644 - 25,950,438 (+)EnsemblGRCm39 Ensembl
GRCm381725,727,703 - 25,731,464 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1725,727,670 - 25,731,464 (+)EnsemblGRCm38mm10GRCm38
MGSCv371725,864,696 - 25,868,401 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361725,455,351 - 25,459,056 (+)NCBIMGSCv36mm8
Celera1726,260,053 - 26,263,758 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1712.83NCBI
Rpusd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544216,423,526 - 16,430,265 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544216,423,526 - 16,426,623 (+)NCBIChiLan1.0ChiLan1.0
RPUSD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2181,027,066 - 1,030,573 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1164,811,081 - 4,814,534 (-)NCBINHGRI_mPanPan1
PanPan1.116800,191 - 803,446 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl16800,191 - 806,007 (-)Ensemblpanpan1.1panPan2
RPUSD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1639,815,405 - 39,818,151 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl639,803,930 - 39,828,899 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha641,080,083 - 41,082,808 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0640,158,538 - 40,161,263 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl640,158,482 - 40,161,260 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1639,847,169 - 39,849,894 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0639,807,382 - 39,810,107 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0640,286,259 - 40,288,984 (+)NCBIUU_Cfam_GSD_1.0
Rpusd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344112,143,327 - 112,146,320 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936501241,232 - 244,366 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936501241,190 - 244,180 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RPUSD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl341,009,717 - 41,013,018 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1341,009,722 - 41,013,013 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2341,464,899 - 41,468,144 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RPUSD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.15704,649 - 708,025 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl5704,519 - 708,058 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606830,426,406 - 30,429,799 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rpusd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249131,589,335 - 1,594,641 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249131,590,158 - 1,594,497 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rpusd1
67 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:97
Count of miRNA genes:80
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000015206
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10129497586Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat


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: ENSRNOT00000015206   ⟹   ENSRNOP00000015206
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1014,751,384 - 14,755,207 (+)Ensembl
Rnor_6.0 Ensembl1015,099,009 - 15,102,960 (+)Ensembl
RefSeq Acc Id: NM_001105774   ⟹   NP_001099244
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,255,876 - 15,259,730 (+)NCBI
mRatBN7.21014,751,357 - 14,755,212 (+)NCBI
Rnor_6.01015,099,113 - 15,102,967 (+)NCBI
Rnor_5.01014,911,797 - 14,915,689 (+)NCBI
RGSC_v3.41014,996,497 - 15,000,351 (+)RGD
Celera1014,420,831 - 14,424,687 (+)RGD
Sequence:
RefSeq Acc Id: XM_006245937   ⟹   XP_006245999
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,255,806 - 15,259,729 (+)NCBI
mRatBN7.21014,751,319 - 14,755,213 (+)NCBI
Rnor_6.01015,099,104 - 15,102,968 (+)NCBI
Rnor_5.01014,911,797 - 14,915,689 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039085363   ⟹   XP_038941291
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,255,834 - 15,259,729 (+)NCBI
mRatBN7.21014,751,310 - 14,754,107 (+)NCBI
RefSeq Acc Id: XM_063268569   ⟹   XP_063124639
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,255,832 - 15,259,729 (+)NCBI
RefSeq Acc Id: NP_001099244   ⟸   NM_001105774
- UniProtKB: A6HD41 (UniProtKB/TrEMBL),   F7F6F2 (UniProtKB/TrEMBL),   B1WC14 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006245999   ⟸   XM_006245937
- Peptide Label: isoform X1
- UniProtKB: A6HD41 (UniProtKB/TrEMBL),   F7F6F2 (UniProtKB/TrEMBL),   B1WC14 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000015206   ⟸   ENSRNOT00000015206
RefSeq Acc Id: XP_038941291   ⟸   XM_039085363
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063124639   ⟸   XM_063268569
- Peptide Label: isoform X2
Protein Domains
Pseudouridine synthase RsuA/RluA-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1WC14-F1-model_v2 AlphaFold B1WC14 1-306 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:1304934 AgrOrtholog
BioCyc Gene G2FUF-25765 BioCyc
Ensembl Genes ENSRNOG00000023639 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000015206.7 UniProtKB/TrEMBL
Gene3D-CATH Pseudouridine synthase UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9028415 IMAGE-MGC_LOAD
InterPro PsdUridine_synth_cat_dom UniProtKB/TrEMBL
  PsdUridine_synth_RsuA/RluD UniProtKB/TrEMBL
  RluA_PseudoU_synthase UniProtKB/TrEMBL
KEGG Report rno:287148 UniProtKB/TrEMBL
MGC_CLONE MGC:187772 IMAGE-MGC_LOAD
NCBI Gene 287148 ENTREZGENE
PANTHER MITOCHONDRIAL RNA PSEUDOURIDINE SYNTHASE UniProtKB/TrEMBL
  RNA PSEUDOURIDYLATE SYNTHASE DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
Pfam PseudoU_synth_2 UniProtKB/TrEMBL
PhenoGen Rpusd1 PhenoGen
RatGTEx ENSRNOG00000023639 RatGTEx
Superfamily-SCOP PsdUridine_synth_cat_dom UniProtKB/TrEMBL
UniProt A6HD41 ENTREZGENE, UniProtKB/TrEMBL
  A6HD42_RAT UniProtKB/TrEMBL
  B1WC14 ENTREZGENE
  F7F6F2 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary B1WC14 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-09-21 Rpusd1  RNA pseudouridine synthase domain containing 1  Rpusd1  RNA pseudouridylate synthase domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Rpusd1  RNA pseudouridylate synthase domain containing 1   Rpusd1_predicted  RNA pseudouridylate synthase domain containing 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Rpusd1_predicted  RNA pseudouridylate synthase domain containing 1 (predicted)  RGD1304934_predicted  similar to RIKEN cDNA 2310051D06 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1304934_predicted  similar to RIKEN cDNA 2310051D06 (predicted)  LOC287148_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC287148_predicted  similar to RIKEN cDNA 2310051D06 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL