Utp20 (UTP20 small subunit processome component) - Rat Genome Database

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Gene: Utp20 (UTP20 small subunit processome component) Rattus norvegicus
Analyze
Symbol: Utp20
Name: UTP20 small subunit processome component
RGD ID: 1560606
Description: Predicted to be involved in rRNA processing. Predicted to be located in plasma membrane. Predicted to be part of 90S preribosome and small-subunit processome. Predicted to be active in nucleolus. Orthologous to human UTP20 (UTP20 small subunit processome component); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC314713; RGD1560606; similar to down-regulated in metastasis; small subunit processome component 20 homolog; UTP20 small subunit (SSU) processome component; UTP20, small subunit (SSU) processome component, homolog; UTP20, small subunit (SSU) processome component, homolog (yeast)
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
mRatBN7.2723,134,630 - 23,215,639 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl723,134,637 - 23,215,632 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx725,129,194 - 25,210,018 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0727,291,898 - 27,372,560 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0727,068,936 - 27,149,757 (-)NCBIRnor_WKY
Rnor_6.0729,296,360 - 29,378,105 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl729,296,963 - 29,378,080 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0729,399,165 - 29,480,171 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4725,419,625 - 25,501,987 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera720,293,710 - 20,374,246 (-)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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
Additional References at PubMed
PMID:16458307   PMID:17498821   PMID:22658674   PMID:22681889  


Genomics

Comparative Map Data
Utp20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2723,134,630 - 23,215,639 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl723,134,637 - 23,215,632 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx725,129,194 - 25,210,018 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0727,291,898 - 27,372,560 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0727,068,936 - 27,149,757 (-)NCBIRnor_WKY
Rnor_6.0729,296,360 - 29,378,105 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl729,296,963 - 29,378,080 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0729,399,165 - 29,480,171 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4725,419,625 - 25,501,987 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera720,293,710 - 20,374,246 (-)NCBICelera
Cytogenetic Map7q13NCBI
UTP20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812101,280,105 - 101,386,618 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl12101,280,105 - 101,386,618 (+)EnsemblGRCh38hg38GRCh38
GRCh3712101,673,883 - 101,780,396 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3612100,198,036 - 100,304,528 (+)NCBINCBI36Build 36hg18NCBI36
Celera12101,339,214 - 101,445,692 (+)NCBICelera
Cytogenetic Map12q23.2NCBI
HuRef1298,734,067 - 98,840,479 (+)NCBIHuRef
CHM1_112101,639,865 - 101,746,373 (+)NCBICHM1_1
T2T-CHM13v2.012101,241,888 - 101,347,734 (+)NCBIT2T-CHM13v2.0
Utp20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391088,582,469 - 88,662,676 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1088,582,469 - 88,662,666 (-)EnsemblGRCm39 Ensembl
GRCm381088,746,607 - 88,826,814 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1088,746,607 - 88,826,804 (-)EnsemblGRCm38mm10GRCm38
MGSCv371088,209,352 - 88,289,559 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361088,175,667 - 88,256,613 (-)NCBIMGSCv36mm8
Celera1090,726,629 - 90,806,960 (-)NCBICelera
Cytogenetic Map10C1NCBI
Utp20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540536,830,176 - 36,909,967 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540536,829,984 - 36,910,149 (+)NCBIChiLan1.0ChiLan1.0
UTP20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112102,265,283 - 102,372,830 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12102,265,283 - 102,372,830 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01298,865,121 - 98,972,914 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
UTP20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11540,291,344 - 40,387,200 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1540,291,390 - 40,387,032 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1540,659,968 - 40,756,261 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01540,945,936 - 41,042,475 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1540,945,935 - 41,041,869 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11540,201,734 - 40,297,982 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01540,310,266 - 40,406,738 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01540,584,482 - 40,681,018 (+)NCBIUU_Cfam_GSD_1.0
Utp20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494519,587,839 - 19,682,872 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649212,598,308 - 12,693,514 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493649212,598,178 - 12,693,279 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UTP20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl582,813,717 - 82,913,155 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1582,810,700 - 82,913,176 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2586,806,041 - 86,907,727 (-)NCBISscrofa10.2Sscrofa10.2susScr3
UTP20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11196,549,046 - 96,657,494 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1196,549,037 - 96,659,699 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037148,345,723 - 148,454,642 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Utp20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247506,526,831 - 6,603,516 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247506,526,692 - 6,603,707 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Utp20
755 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:179
Count of miRNA genes:133
Interacting mature miRNAs:147
Transcripts:ENSRNOT00000008317
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
70207Niddm31Non-insulin dependent diabetes mellitus QTL 313.9blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)71816950526029351Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)71903280735526300Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)72055570529891047Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat

Markers in Region
RH129580  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2723,134,803 - 23,134,994 (+)MAPPERmRatBN7.2
Rnor_6.0729,297,086 - 29,297,276NCBIRnor6.0
Rnor_5.0729,399,339 - 29,399,529UniSTSRnor5.0
RGSC_v3.4725,419,799 - 25,419,989UniSTSRGSC3.4
Celera720,293,884 - 20,294,074UniSTS
RH 3.4 Map7133.0UniSTS
Cytogenetic Map7q13UniSTS
RH142917  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2723,183,800 - 23,183,930 (+)MAPPERmRatBN7.2
Rnor_6.0729,346,273 - 29,346,402NCBIRnor6.0
Rnor_5.0729,448,526 - 29,448,655UniSTSRnor5.0
RGSC_v3.4725,470,312 - 25,470,441UniSTSRGSC3.4
Celera720,342,706 - 20,342,835UniSTS
Cytogenetic Map7q13UniSTS
RH144482  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2723,134,207 - 23,134,422 (+)MAPPERmRatBN7.2
Rnor_6.0729,296,490 - 29,296,704NCBIRnor6.0
Rnor_5.0729,398,743 - 29,398,957UniSTSRnor5.0
RGSC_v3.4725,419,203 - 25,419,417UniSTSRGSC3.4
Celera720,293,288 - 20,293,502UniSTS
RH 3.4 Map7120.26UniSTS
Cytogenetic Map7q13UniSTS
RH138562  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2723,183,823 - 23,184,000 (+)MAPPERmRatBN7.2
Rnor_6.0729,346,296 - 29,346,472NCBIRnor6.0
Rnor_5.0729,448,549 - 29,448,725UniSTSRnor5.0
RGSC_v3.4725,470,335 - 25,470,511UniSTSRGSC3.4
Celera720,342,729 - 20,342,905UniSTS
RH 3.4 Map7133.0UniSTS
Cytogenetic Map7q13UniSTS


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 30 14 19 14 54 21 37 9
Low 2 27 27 27 27 8 11 20 14 4 2 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008317   ⟹   ENSRNOP00000008317
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl723,134,637 - 23,215,632 (-)Ensembl
Rnor_6.0 Ensembl729,296,963 - 29,378,080 (-)Ensembl
RefSeq Acc Id: NM_001191779   ⟹   NP_001178708
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,134,630 - 23,215,454 (-)NCBI
Rnor_6.0729,296,912 - 29,377,920 (-)NCBI
Rnor_5.0729,399,165 - 29,480,171 (-)NCBI
Celera720,293,710 - 20,374,246 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006241227   ⟹   XP_006241289
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,134,630 - 23,215,638 (-)NCBI
Rnor_6.0729,296,360 - 29,378,105 (-)NCBI
Rnor_5.0729,399,165 - 29,480,171 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039079040   ⟹   XP_038934968
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2723,150,466 - 23,215,639 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001178708 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241289 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934968 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM16994 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001178708   ⟸   NM_001191779
- UniProtKB: F1LXT3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241289   ⟸   XM_006241227
- Peptide Label: isoform X1
- UniProtKB: F1LXT3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008317   ⟸   ENSRNOT00000008317
RefSeq Acc Id: XP_038934968   ⟸   XM_039079040
- Peptide Label: isoform X2
Protein Domains
DRIM

Transcriptome

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

Promoters
RGD ID:13695132
Promoter ID:EPDNEW_R5657
Type:multiple initiation site
Name:Utp20_1
Description:UTP20 small subunit processome component
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_6.0729,378,083 - 29,378,143EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560606 AgrOrtholog
BioCyc Gene G2FUF-34498 BioCyc
Ensembl Genes ENSRNOG00000005823 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008317 ENTREZGENE
  ENSRNOP00000008317.8 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008317 ENTREZGENE
  ENSRNOT00000008317.8 UniProtKB/TrEMBL
InterPro ARM-type_fold UniProtKB/TrEMBL
  DRIM UniProtKB/TrEMBL
NCBI Gene 314713 ENTREZGENE
Pfam DRIM UniProtKB/TrEMBL
PhenoGen Utp20 PhenoGen
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniProt F1LXT3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Utp20  UTP20 small subunit processome component  Utp20  UTP20 small subunit (SSU) processome component  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-10-28 Utp20  UTP20 small subunit (SSU) processome component  Utp20  UTP20, small subunit (SSU) processome component, homolog (yeast)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-28 Utp20  UTP20, small subunit (SSU) processome component, homolog (yeast)  RGD1560606_predicted  similar to down-regulated in metastasis (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560606_predicted  similar to down-regulated in metastasis (predicted)  LOC314713  similar to down-regulated in metastasis  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC314713  similar to down-regulated in metastasis      Symbol and Name status set to provisional 70820 PROVISIONAL