Usb1 (U6 snRNA biogenesis phosphodiesterase 1) - Rat Genome Database

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Gene: Usb1 (U6 snRNA biogenesis phosphodiesterase 1) Rattus norvegicus
Analyze
Symbol: Usb1
Name: U6 snRNA biogenesis phosphodiesterase 1
RGD ID: 1305215
Description: Predicted to enable poly(U)-specific exoribonuclease activity, producing 3' uridine cyclic phosphate ends. Predicted to be involved in RNA splicing and U6 snRNA 3'-end processing. Predicted to be located in intercellular bridge and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in poikiloderma with neutropenia. Orthologous to human USB1 (U6 snRNA biogenesis phosphodiesterase 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; paracetamol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 3'-5' RNA exonuclease USB1; hypothetical protein LOC307643; LOC307643; putative U6 snRNA phosphodiesterase; RGD1305215; similar to expressed sequence AA960436; U6 snRNA biogenesis 1; U6 snRNA phosphodiesterase; U6 snRNA phosphodiesterase 1; UPF0406 protein C16orf57 homolog
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
mRatBN7.2199,689,313 - 9,702,306 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl199,689,316 - 9,702,302 (-)Ensembl
Rnor_6.01910,105,750 - 10,118,701 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1910,105,701 - 10,119,128 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01910,089,670 - 10,102,534 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41910,148,223 - 10,162,086 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11910,153,050 - 10,166,912 (-)NCBI
Celera199,582,087 - 9,595,145 (-)NCBICelera
Cytogenetic Map19p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
intercellular bridge  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IBA,ISO,ISS)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
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:15489334   PMID:22899009   PMID:23190533  


Genomics

Comparative Map Data
Usb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2199,689,313 - 9,702,306 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl199,689,316 - 9,702,302 (-)Ensembl
Rnor_6.01910,105,750 - 10,118,701 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1910,105,701 - 10,119,128 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01910,089,670 - 10,102,534 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41910,148,223 - 10,162,086 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11910,153,050 - 10,166,912 (-)NCBI
Celera199,582,087 - 9,595,145 (-)NCBICelera
Cytogenetic Map19p13NCBI
USB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381657,999,603 - 58,021,618 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1657,999,546 - 58,021,618 (+)EnsemblGRCh38hg38GRCh38
GRCh371658,033,507 - 58,055,522 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361656,592,806 - 56,613,023 (+)NCBINCBI36hg18NCBI36
Celera1642,532,629 - 42,552,834 (+)NCBI
Cytogenetic Map16q21NCBI
HuRef1643,902,322 - 43,922,661 (+)NCBIHuRef
CHM1_11659,442,351 - 59,462,601 (+)NCBICHM1_1
T2T-CHM13v2.01663,794,892 - 63,816,894 (+)NCBI
Usb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39896,058,006 - 96,074,141 (+)NCBIGRCm39mm39
GRCm39 Ensembl896,058,912 - 96,074,135 (+)Ensembl
GRCm38895,331,413 - 95,347,513 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl895,332,284 - 95,347,507 (+)EnsemblGRCm38mm10GRCm38
MGSCv37897,856,184 - 97,871,413 (+)NCBIGRCm37mm9NCBIm37
MGSCv36898,221,469 - 98,236,638 (+)NCBImm8
Celera899,653,251 - 99,668,578 (+)NCBICelera
Cytogenetic Map8C5NCBI
Usb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543315,572,881 - 15,579,509 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495543315,572,884 - 15,580,108 (+)NCBIChiLan1.0ChiLan1.0
USB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11657,408,841 - 57,430,665 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1657,408,841 - 57,430,665 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01638,277,987 - 38,300,863 (+)NCBIMhudiblu_PPA_v0panPan3
USB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1258,535,173 - 58,549,877 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl258,536,142 - 58,549,778 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha255,164,980 - 55,179,704 (-)NCBI
ROS_Cfam_1.0259,073,911 - 59,088,638 (-)NCBI
ROS_Cfam_1.0 Ensembl259,074,602 - 59,104,365 (-)Ensembl
UMICH_Zoey_3.1255,905,328 - 55,920,029 (-)NCBI
UNSW_CanFamBas_1.0256,912,825 - 56,927,141 (-)NCBI
UU_Cfam_GSD_1.0257,805,909 - 57,820,814 (-)NCBI
Usb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934949,641,157 - 49,655,894 (-)NCBI
SpeTri2.0NW_0049364759,933,607 - 9,947,910 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
USB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl619,852,014 - 19,874,020 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1619,852,020 - 19,874,016 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2617,904,319 - 17,921,446 (+)NCBISscrofa10.2Sscrofa10.2susScr3
USB1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1543,932,208 - 43,956,719 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl543,932,847 - 43,957,074 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604732,222,064 - 32,245,989 (-)NCBIVero_WHO_p1.0
Usb1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474628,151,208 - 28,166,438 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462474628,152,239 - 28,166,062 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:156
Count of miRNA genes:108
Interacting mature miRNAs:132
Transcripts:ENSRNOT00000017960
Prediction methods: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.


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 1 16 6 6 1 6 34 20 28 3
Low 2 27 51 35 18 35 8 11 40 15 13 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000017960   ⟹   ENSRNOP00000017960
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl199,689,316 - 9,702,302 (-)Ensembl
Rnor_6.0 Ensembl1910,105,701 - 10,119,128 (-)Ensembl
RefSeq Acc Id: NM_001014013   ⟹   NP_001014035
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,689,313 - 9,702,275 (-)NCBI
Rnor_6.01910,105,750 - 10,118,701 (-)NCBI
Rnor_5.01910,089,670 - 10,102,534 (-)NCBI
RGSC_v3.41910,148,223 - 10,162,086 (-)RGD
Celera199,582,087 - 9,595,145 (-)RGD
Sequence:
RefSeq Acc Id: XM_039097697   ⟹   XP_038953625
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2199,689,313 - 9,702,306 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001014035 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953625 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88280 (Get FASTA)   NCBI Sequence Viewer  
  EDL87289 (Get FASTA)   NCBI Sequence Viewer  
  Q5I0I5 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001014035   ⟸   NM_001014013
- UniProtKB: Q5I0I5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017960   ⟸   ENSRNOT00000017960
RefSeq Acc Id: XP_038953625   ⟸   XM_039097697
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5I0I5-F1-model_v2 AlphaFold Q5I0I5 1-267 view protein structure

Transcriptome

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

Promoters
RGD ID:13700930
Promoter ID:EPDNEW_R11454
Type:initiation region
Name:Usb1_1
Description:U6 snRNA biogenesis phosphodiesterase 1
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_6.01910,118,743 - 10,118,803EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
19 10093136 10093137 C G snv IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305215 AgrOrtholog
BioCyc Gene G2FUF-6530 BioCyc
Ensembl Genes ENSRNOG00000013216 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000017960 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000017960 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7383193 IMAGE-MGC_LOAD
InterPro cNuc_Pdiesterase UniProtKB/Swiss-Prot
  Usb1 UniProtKB/Swiss-Prot
KEGG Report rno:307643 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109139 IMAGE-MGC_LOAD
NCBI Gene 307643 ENTREZGENE
PANTHER PTHR13522 UniProtKB/Swiss-Prot
Pfam HVSL UniProtKB/Swiss-Prot
PhenoGen Usb1 PhenoGen
Superfamily-SCOP SSF55144 UniProtKB/Swiss-Prot
UniProt Q5I0I5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-04-13 Usb1  U6 snRNA biogenesis phosphodiesterase 1  Usb1  U6 snRNA biogenesis 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-10 Usb1  U6 snRNA biogenesis 1  RGD1305215  similar to expressed sequence AA960436  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1305215  similar to expressed sequence AA960436  RGD1305215_predicted  similar to expressed sequence AA960436 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1305215_predicted  similar to expressed sequence AA960436 (predicted)  LOC307643_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC307643_predicted  similar to expressed sequence AA960436 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL