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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8199,695,370 - 9,708,329 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl199,694,267 - 9,708,329 (-)EnsemblGRCr8
mRatBN7.2199,689,313 - 9,702,306 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl199,689,316 - 9,702,302 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx199,654,292 - 9,667,274 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01910,421,121 - 10,434,103 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0199,707,450 - 9,720,434 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01910,105,750 - 10,118,701 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1910,105,701 - 10,119,128 (-)Ensemblrn6Rnor6.0
Rnor_5.01910,089,670 - 10,102,534 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41910,148,223 - 10,162,086 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera199,582,087 - 9,595,145 (-)NCBICelera
RGSC_v3.11910,153,050 - 10,166,912 (-)NCBI
Cytogenetic Map19p13NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
RNA splicing  (IEA,ISO,ISS)
snRNA 3'-end processing  (IEA,ISO,ISS)
U6 snRNA 3'-end processing  (IBA,IEA,ISO,ISS)

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,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
GRCr8199,695,370 - 9,708,329 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl199,694,267 - 9,708,329 (-)EnsemblGRCr8
mRatBN7.2199,689,313 - 9,702,306 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl199,689,316 - 9,702,302 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx199,654,292 - 9,667,274 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01910,421,121 - 10,434,103 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0199,707,450 - 9,720,434 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01910,105,750 - 10,118,701 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1910,105,701 - 10,119,128 (-)Ensemblrn6Rnor6.0
Rnor_5.01910,089,670 - 10,102,534 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41910,148,223 - 10,162,086 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera199,582,087 - 9,595,145 (-)NCBICelera
RGSC_v3.11910,153,050 - 10,166,912 (-)NCBI
Cytogenetic Map19p13NCBI
USB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381657,999,603 - 58,021,618 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1657,999,546 - 58,021,618 (+)Ensemblhg38GRCh38
GRCh371658,033,507 - 58,055,522 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361656,592,806 - 56,613,023 (+)NCBIBuild 36Build 36hg18NCBI36
Celera1642,532,629 - 42,552,834 (+)NCBICelera
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 (+)NCBIT2T-CHM13v2.0
Usb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39896,058,006 - 96,074,137 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl896,058,912 - 96,074,135 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38895,331,413 - 95,347,513 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl895,332,284 - 95,347,507 (+)Ensemblmm10GRCm38
MGSCv37897,856,184 - 97,871,413 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36898,221,469 - 98,236,638 (+)NCBIMGSCv36mm8
Celera899,653,251 - 99,668,578 (+)NCBICelera
Cytogenetic Map8C5NCBI
cM Map847.12NCBI
Usb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543315,572,881 - 15,579,509 (+)Ensembl
ChiLan1.0NW_00495543315,572,884 - 15,580,108 (+)NCBIChiLan1.0ChiLan1.0
USB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21867,472,463 - 67,495,273 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11673,393,257 - 73,416,149 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01638,277,987 - 38,300,863 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11657,408,841 - 57,430,665 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1657,408,841 - 57,430,665 (+)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha255,164,980 - 55,179,704 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0259,073,911 - 59,088,638 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl259,074,602 - 59,104,365 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1255,905,328 - 55,920,029 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0256,912,825 - 56,927,141 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0257,805,909 - 57,820,814 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Usb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934949,641,157 - 49,655,894 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364759,933,163 - 9,947,970 (+)EnsemblSpeTri2.0 Ensembl
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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl543,932,847 - 43,957,074 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604732,222,064 - 32,245,989 (-)NCBIVero_WHO_p1.0Vero_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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474628,152,239 - 28,166,062 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Usb1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1172,193,571 - 2,205,679 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Usb1
53 total Variants
miRNA Target Status (No longer updated)

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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131969901Rat
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)19799775052997750Rat
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124694445Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19799775052997750Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19799775052997750Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19799775052997750Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)19574806450748064Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127361636Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat


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 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000017960   ⟹   ENSRNOP00000017960
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl199,695,377 - 9,708,329 (-)Ensembl
mRatBN7.2 Ensembl199,689,316 - 9,702,302 (-)Ensembl
Rnor_6.0 Ensembl1910,105,701 - 10,119,128 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000122621   ⟹   ENSRNOP00000109965
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl199,694,267 - 9,708,329 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000123570   ⟹   ENSRNOP00000110944
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl199,696,614 - 9,708,329 (-)Ensembl
RefSeq Acc Id: NM_001014013   ⟹   NP_001014035
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8199,695,370 - 9,708,329 (-)NCBI
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:
Protein Sequences
Protein RefSeqs NP_001014035 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88280 (Get FASTA)   NCBI Sequence Viewer  
  EDL87289 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017960
  ENSRNOP00000017960.3
GenBank Protein Q5I0I5 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001014035   ⟸   NM_001014013
- UniProtKB: Q5I0I5 (UniProtKB/Swiss-Prot),   A6JY12 (UniProtKB/TrEMBL),   A6JY11 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000017960   ⟸   ENSRNOT00000017960
Ensembl Acc Id: ENSRNOP00000110944   ⟸   ENSRNOT00000123570
Ensembl Acc Id: ENSRNOP00000109965   ⟸   ENSRNOT00000122621

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

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 Transcript ENSRNOT00000017960 ENTREZGENE
  ENSRNOT00000017960.6 UniProtKB/Swiss-Prot
Gene3D-CATH Cyclic phosphodiesterase 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
  U6 SNRNA PHOSPHODIESTERASE UniProtKB/Swiss-Prot
Pfam HVSL UniProtKB/Swiss-Prot
PhenoGen Usb1 PhenoGen
RatGTEx ENSRNOG00000013216 RatGTEx
Superfamily-SCOP SSF55144 UniProtKB/Swiss-Prot
UniProt A0ABK0M3R9_RAT UniProtKB/TrEMBL
  A0ABK0M6M0_RAT UniProtKB/TrEMBL
  A6JY11 ENTREZGENE, UniProtKB/TrEMBL
  A6JY12 ENTREZGENE, UniProtKB/TrEMBL
  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