Snora5c (small nucleolar RNA, H/ACA box 5C) - Rat Genome Database

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Gene: Snora5c (small nucleolar RNA, H/ACA box 5C) Mus musculus
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Symbol: Snora5c
Name: small nucleolar RNA, H/ACA box 5C
RGD ID: 2302594
MGI Page MGI
Description: ASSOCIATED WITH pleomorphic xanthoastrocytoma (ortholog); INTERACTS WITH aldehydo-D-glucose; D-glucose; glucose
Type: snorna
RefSeq Status: VALIDATED
Previously known as: MBI-8; MBI-80
RGD Orthologs
Human
Rat
Dog
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,570,319 - 6,570,419 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl116,570,319 - 6,570,454 (-)EnsemblGRCm39 Ensembl
GRCm38116,620,319 - 6,620,419 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,620,319 - 6,620,454 (-)EnsemblGRCm38mm10GRCm38
Celera1118,693,545 - 18,693,645 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map114.6NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Snora5cMousepleomorphic xanthoastrocytoma  ISORGD:16027548554872ClinVar Annotator: match by term: Pleomorphic xanthoastrocytomaClinVarPMID:28299358

1 to 10 of 10 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Snora5cMouse(-)-epigallocatechin 3-gallate multiple interactionsISORGD:16027546480464[potassium chromate(VI) co-treated with epigallocatechin gallate] results in increased expression of SNORA5C mRNACTDPMID:22079256
Snora5cMousealdehydo-D-glucose increases expressionEXP 6480464Glucose results in increased expression of SNORA5C mRNACTDPMID:31525975
Snora5cMouseD-glucose increases expressionEXP 6480464Glucose results in increased expression of SNORA5C mRNACTDPMID:31525975
Snora5cMouseDDT decreases expressionISORGD:16027546480464DDT results in decreased expression of SNORA5C mRNACTDPMID:25014179
Snora5cMouseglucose increases expressionEXP 6480464Glucose results in increased expression of SNORA5C mRNACTDPMID:31525975
Snora5cMousepotassium chromate increases expressionISORGD:16027546480464potassium chromate(VI) results in increased expression of SNORA5C mRNACTDPMID:22079256
Snora5cMousepotassium chromate multiple interactionsISORGD:16027546480464[potassium chromate(VI) co-treated with epigallocatechin gallate] results in increased expression of SNORA5C mRNACTDPMID:22079256
Snora5cMousetitanium dioxide decreases methylationEXP 6480464titanium dioxide results in decreased methylation of SNORA5C promoterCTDPMID:35295148
Snora5cMousetrovafloxacin increases expressionEXP 6480464trovafloxacin results in increased expression of SNORA5C mRNACTDPMID:35537566
Snora5cMousevalproic acid increases methylationISORGD:16027546480464Valproic Acid results in increased methylation of SNORA5C geneCTDPMID:29154799

1 to 10 of 10 rows

Biological Process

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Snora5cMousebiological_process involved_inND 2290270 MGIGO_REF:0000015

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Snora5cMousecellular_component is_active_inND 2290270 MGIGO_REF:0000015

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Snora5cMousemolecular_function enablesND 2290270 MGIGO_REF:0000015


#
Reference Title
Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
PMID:11387227   PMID:11424213  



Snora5c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,570,319 - 6,570,419 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl116,570,319 - 6,570,454 (-)EnsemblGRCm39 Ensembl
GRCm38116,620,319 - 6,620,419 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,620,319 - 6,620,454 (-)EnsemblGRCm38mm10GRCm38
Celera1118,693,545 - 18,693,645 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map114.6NCBI
SNORA5C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38745,104,906 - 45,105,042 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl745,104,906 - 45,105,042 (-)EnsemblGRCh38hg38GRCh38
GRCh37745,144,505 - 45,144,641 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36745,111,030 - 45,111,166 (-)NCBINCBI36Build 36hg18NCBI36
Celera745,243,348 - 45,243,484 (-)NCBICelera
Cytogenetic Map7p13NCBI
HuRef745,028,310 - 45,028,446 (-)NCBIHuRef
CHM1_1745,148,194 - 45,148,330 (-)NCBICHM1_1
T2T-CHM13v2.0745,265,707 - 45,265,843 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2745,183,675 - 45,183,811 (-)NCBI
Snora5c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81485,701,133 - 85,701,269 (-)NCBIGRCr8
mRatBN7.21481,487,218 - 81,487,354 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1481,487,218 - 81,487,354 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl1486,882,041 - 86,882,177 (-)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map14q21NCBI
LOC119869668
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha162,632,714 - 2,632,850 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01614,228,036 - 14,228,172 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1614,228,036 - 14,228,172 (+)EnsemblROS_Cfam_1.0 Ensembl
UNSW_CanFamBas_1.01613,860,944 - 13,861,080 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01613,840,402 - 13,840,538 (+)NCBIUU_Cfam_GSD_1.0

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Variants in Snora5c
1 total Variants

Predicted Target Of
Summary Value
Count of predictions:262
Count of miRNA genes:232
Interacting mature miRNAs:257
Transcripts:ENSMUST00000083752
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.


1 to 10 of 19 rows
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
1300599Cocrb11_mcocaine related behavior 11 (mouse)Not determined11267035536671472Mouse
26884446Sklq10_mskull length QTL 10, 10 week (mouse)11325000062890826Mouse
1300661Lmr6_mleishmaniasis resistance 6 (mouse)Not determined11125976374Mouse
13208559Wght10_mweight 10 (mouse)11395000088890826Mouse
13208558Lgth12_mbody length 12 (mouse)11395000094890826Mouse
27095925Pglq5_mpelvic girdle length QTL 5, 5 week (mouse)11325000019750000Mouse
27226741Metcl5_mmetatarsal-calcaneal length 5, 5 week (mouse)11465000046290827Mouse
1357722Vtbt11_mvertebral trabecular bone trait 11 (mouse)Not determined11123880487Mouse
27226735Metcl16_mmetatarsal-calcaneal length 16, 16 week (mouse)11525000035090827Mouse
10044008Hbnr15_mHeligmosomoides bakeri nematode resistance 15 (mouse)Not determined1122705234227232Mouse

1 to 10 of 19 rows






Ensembl Acc Id: ENSMUST00000083752
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,570,319 - 6,570,454 (-)Ensembl
GRCm38.p6 Ensembl116,620,319 - 6,620,454 (-)Ensembl
RefSeq Acc Id: NR_034042
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39116,570,319 - 6,570,419 (-)NCBI
GRCm38116,620,319 - 6,620,419 (-)ENTREZGENE
Celera1118,693,545 - 18,693,645 (-)ENTREZGENE
cM Map11 ENTREZGENE
Sequence:
RGD ID:8673918
Promoter ID:EPDNEW_M14990
Type:single initiation site
Name:Snora5c_1
Description:Mus musculus small nucleolar RNA, H/ACA box 5C , small nucleolarRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38116,620,510 - 6,620,570EPDNEW


Database
Acc Id
Source(s)
Ensembl Genes ENSMUSG00000065686 Ensembl
MGD MGI:3819509 ENTREZGENE
NCBI Gene 100217467 ENTREZGENE
PhenoGen Snora5c PhenoGen
RNAcentral URS000071AC4F RNACentral
  URS0000E60A74 RNACentral