Utp25 (UTP25 small subunit processome component) - Rat Genome Database

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Gene: Utp25 (UTP25 small subunit processome component) Rattus norvegicus
Analyze
Symbol: Utp25
Name: UTP25 small subunit processome component
RGD ID: 1359148
Description: Predicted to enable U3 snoRNA binding activity and rRNA binding activity. Predicted to be involved in several processes, including maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); protein destabilization; and protein localization to nucleolus. Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. Orthologous to human UTP25 (UTP25 small subunit processome component); INTERACTS WITH (+)-schisandrin B; amphetamine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Def; Diexf; digestive organ expansion factor homolog; digestive organ expansion factor homolog (zebrafish); LOC305076; novel putative protein similar to YIL091C yeast hypothetical 84 kD protein from SGA1-KTR7; similar to hypothetical protein MGC29875; U3 small nucleolar RNA-associated protein 25 homolog; UTP25, small subunit processor component
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
GRCr813107,159,092 - 107,180,361 (-)NCBIGRCr8
mRatBN7.213104,630,390 - 104,651,681 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13104,630,391 - 104,651,662 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13107,148,008 - 107,169,277 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013108,531,858 - 108,553,127 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013105,749,825 - 105,771,095 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.013111,828,052 - 111,849,654 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13111,828,043 - 111,849,653 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013116,382,860 - 116,404,451 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413108,945,112 - 108,966,381 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.113109,134,216 - 109,155,439 (-)NCBI
Celera13104,060,438 - 104,081,707 (-)NCBICelera
Cytogenetic Map13q27NCBI
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

Cellular Component
nucleolus  (IBA,ISO,ISS)
small-subunit processome  (IBA)

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. 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. 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:22658674   PMID:23357851   PMID:29262616  


Genomics

Comparative Map Data
Utp25
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr813107,159,092 - 107,180,361 (-)NCBIGRCr8
mRatBN7.213104,630,390 - 104,651,681 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13104,630,391 - 104,651,662 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13107,148,008 - 107,169,277 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.013108,531,858 - 108,553,127 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.013105,749,825 - 105,771,095 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.013111,828,052 - 111,849,654 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13111,828,043 - 111,849,653 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013116,382,860 - 116,404,451 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413108,945,112 - 108,966,381 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.113109,134,216 - 109,155,439 (-)NCBI
Celera13104,060,438 - 104,081,707 (-)NCBICelera
Cytogenetic Map13q27NCBI
UTP25
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381209,827,972 - 209,857,565 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1209,827,972 - 209,857,565 (+)EnsemblGRCh38hg38GRCh38
GRCh371210,001,317 - 210,030,910 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361208,067,956 - 208,097,531 (+)NCBINCBI36Build 36hg18NCBI36
Celera1183,232,203 - 183,261,798 (+)NCBICelera
Cytogenetic Map1q32.2NCBI
HuRef1180,676,427 - 180,706,025 (+)NCBIHuRef
CHM1_11211,273,584 - 211,303,174 (+)NCBICHM1_1
T2T-CHM13v2.01209,074,743 - 209,104,338 (+)NCBIT2T-CHM13v2.0
Utp25
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391192,786,707 - 192,812,603 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1192,773,412 - 192,812,580 (-)EnsemblGRCm39 Ensembl
GRCm381193,104,399 - 193,130,283 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1193,091,104 - 193,130,272 (-)EnsemblGRCm38mm10GRCm38
MGSCv371194,930,597 - 194,956,445 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361194,805,127 - 194,830,975 (-)NCBIMGSCv36mm8
Celera1199,979,507 - 200,005,362 (-)NCBICelera
Cytogenetic Map1H6NCBI
cM Map197.56NCBI
Utp25
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554892,339,745 - 2,387,103 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554892,362,290 - 2,387,162 (-)NCBIChiLan1.0ChiLan1.0
UTP25
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2139,548,962 - 39,574,522 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1139,515,382 - 39,540,687 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01185,403,715 - 185,433,830 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11190,268,857 - 190,292,729 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1190,268,857 - 190,292,980 (+)Ensemblpanpan1.1panPan2
UTP25
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.178,477,026 - 8,512,713 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl78,488,350 - 8,512,705 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha78,065,263 - 8,090,352 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.078,188,707 - 8,214,441 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl78,188,839 - 8,215,357 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.178,118,398 - 8,143,450 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.078,215,411 - 8,240,320 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.078,242,865 - 8,266,776 (-)NCBIUU_Cfam_GSD_1.0
Utp25
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934466,003,992 - 66,028,584 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365573,223,470 - 3,268,888 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365573,244,274 - 3,268,853 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
UTP25
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9133,105,063 - 133,141,217 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19133,115,177 - 133,141,258 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29146,382,511 - 146,400,265 (-)NCBISscrofa10.2Sscrofa10.2susScr3
UTP25
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12519,601,165 - 19,625,274 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2519,600,266 - 19,625,229 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605520,200,305 - 20,224,419 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Utp25
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248072,145,963 - 2,166,885 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248072,069,501 - 2,166,859 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Utp25
57 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:183
Count of miRNA genes:136
Interacting mature miRNAs:145
Transcripts:ENSRNOT00000006395
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
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat

Markers in Region
BF392838  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.213104,640,515 - 104,641,120 (+)MAPPERmRatBN7.2
Rnor_6.013111,838,486 - 111,839,090NCBIRnor6.0
Rnor_5.013116,393,294 - 116,393,898UniSTSRnor5.0
RGSC_v3.413108,955,236 - 108,955,840UniSTSRGSC3.4
Celera13104,070,562 - 104,071,166UniSTS
RH 3.4 Map13757.6UniSTS
Cytogenetic Map13q27UniSTS


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 2 24 30 16 19 16 1 1 67 22 36 11 1
Low 1 19 27 25 25 7 10 7 13 5 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006395   ⟹   ENSRNOP00000006395
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl13104,630,391 - 104,651,662 (-)Ensembl
Rnor_6.0 Ensembl13111,828,043 - 111,849,653 (-)Ensembl
RefSeq Acc Id: NM_001013986   ⟹   NP_001014008
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813107,159,092 - 107,180,361 (-)NCBI
mRatBN7.213104,630,390 - 104,651,662 (-)NCBI
Rnor_6.013111,828,360 - 111,849,631 (-)NCBI
Rnor_5.013116,382,860 - 116,404,451 (-)NCBI
RGSC_v3.413108,945,112 - 108,966,381 (-)RGD
Celera13104,060,438 - 104,081,707 (-)RGD
Sequence:
RefSeq Acc Id: XM_063272402   ⟹   XP_063128472
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr813107,159,092 - 107,176,847 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001014008 (Get FASTA)   NCBI Sequence Viewer  
  XP_063128472 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH87114 (Get FASTA)   NCBI Sequence Viewer  
  EDL95025 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006395
  ENSRNOP00000006395.4
  ENSRNOP00055015056
  ENSRNOP00060018843
  ENSRNOP00065004502
GenBank Protein Q5M9G7 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001014008   ⟸   NM_001013986
- UniProtKB: Q5M9G7 (UniProtKB/Swiss-Prot),   A6JH19 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006395   ⟸   ENSRNOT00000006395
RefSeq Acc Id: XP_063128472   ⟸   XM_063272402
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5M9G7-F1-model_v2 AlphaFold Q5M9G7 1-763 view protein structure

Transcriptome

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

Promoters
RGD ID:13699124
Promoter ID:EPDNEW_R9649
Type:initiation region
Name:Diexf_1
Description:digestive organ expansion factor homolog
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_6.013111,849,610 - 111,849,670EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359148 AgrOrtholog
BioCyc Gene G2FUF-16797 BioCyc
Ensembl Genes ENSRNOG00000004789 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055011024 UniProtKB/Swiss-Prot
  ENSRNOG00060013865 UniProtKB/Swiss-Prot
  ENSRNOG00065004393 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000006395 ENTREZGENE
  ENSRNOT00000006395.7 UniProtKB/Swiss-Prot
  ENSRNOT00055018676 UniProtKB/Swiss-Prot
  ENSRNOT00060023691 UniProtKB/Swiss-Prot
  ENSRNOT00065006384 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7193786 IMAGE-MGC_LOAD
InterPro Digest_organ_expansion_fac-prd UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UTP25 UniProtKB/TrEMBL
KEGG Report rno:305076 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:94741 IMAGE-MGC_LOAD
NCBI Gene 305076 ENTREZGENE
PANTHER ORF PROTEIN-RELATED UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
  U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 25 HOMOLOG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam UTP25 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Utp25 PhenoGen
RatGTEx ENSRNOG00000004789 RatGTEx
  ENSRNOG00055011024 RatGTEx
  ENSRNOG00060013865 RatGTEx
  ENSRNOG00065004393 RatGTEx
Superfamily-SCOP P-loop containing nucleoside triphosphate hydrolases UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A6JH19 ENTREZGENE, UniProtKB/TrEMBL
  DIEXF_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-03-14 Utp25  UTP25 small subunit processome component  Utp25  UTP25, small subunit processor component  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2018-05-07 Utp25  UTP25, small subunit processor component  Diexf  digestive organ expansion factor homolog (zebrafish)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-05-25 Diexf   digestive organ expansion factor homolog (zebrafish)   LOC305076  similar to hypothetical protein MGC29875; novel putative protein similar to YIL091C yeast hypothetical 84 kD protein from SGA1-KTR7  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC305076  similar to hypothetical protein MGC29875; novel putative protein similar to YIL091C yeast hypothetical 84 kD protein from SGA1-KTR7      Symbol and Name status set to provisional 70820 PROVISIONAL