Snord89 (small nucleolar RNA, C/D box 89) - Rat Genome Database

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Gene: Snord89 (small nucleolar RNA, C/D box 89) Mus musculus
Analyze
Symbol: Snord89
Name: small nucleolar RNA, C/D box 89
RGD ID: 2302598
MGI Page MGI
Description: INTERACTS WITH buta-1,3-diene; trovafloxacin; antirheumatic drug (ortholog)
Type: snorna
RefSeq Status: VALIDATED
Previously known as: MBII-2; MBII-289
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
GRCm39139,587,828 - 39,587,921 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl139,587,826 - 39,587,935 (-)EnsemblGRCm39 Ensembl
GRCm38139,548,747 - 39,548,840 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl139,548,745 - 39,548,854 (-)EnsemblGRCm38mm10GRCm38
MGSCv37139,605,592 - 39,605,685 (-)NCBIGRCm37MGSCv37mm9NCBIm37
Celera139,343,294 - 39,343,387 (-)NCBICelera
Cytogenetic Map1BNCBI
cM Map118.32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


1 to 15 of 15 rows

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Snord89Mouseantirheumatic drug decreases expressionISOSNORD89 (Homo sapiens)6480464Antirheumatic Agents results in decreased expression of SNORD89 mRNACTDPMID:24449571
Snord89Mousebenzo[a]pyrene decreases methylationISOSNORD89 (Homo sapiens)6480464Benzo(a)pyrene results in decreased methylation of SNORD89 promoterCTDPMID:27901495
Snord89Mousebisphenol A affects expressionISOSNORD89 (Homo sapiens)6480464bisphenol A affects the expression of SNORD89 mRNACTDPMID:30903817
Snord89Mousebuta-1,3-diene decreases expressionEXP 64804641 and 3-butadiene results in decreased expression of SNORD89 mRNACTDPMID:29038090
Snord89Mousecadmium dichloride increases expressionISOSNORD89 (Homo sapiens)6480464Cadmium Chloride results in increased expression of SNORD89 mRNACTDPMID:26472689
Snord89Mousecisplatin decreases expressionISOSNORD89 (Homo sapiens)6480464Cisplatin results in decreased expression of SNORD89 mRNACTDPMID:27392435
Snord89Mousedoxorubicin increases expressionISOSNORD89 (Homo sapiens)6480464Doxorubicin results in increased expression of SNORD89 mRNACTDPMID:29803840
Snord89Mouseethyl methanesulfonate decreases expressionISOSNORD89 (Homo sapiens)6480464Ethyl Methanesulfonate results in decreased expression of SNORD89 mRNACTDPMID:23649840
Snord89Mouselipopolysaccharide multiple interactionsISOSNORD89 (Homo sapiens)6480464[S-(1 and 2-dichlorovinyl)cysteine affects the susceptibility to Lipopolysaccharides] which results in increased expression of SNORD89 mRNACTDPMID:35811015
Snord89Mousemethyl methanesulfonate decreases expressionISOSNORD89 (Homo sapiens)6480464Methyl Methanesulfonate results in decreased expression of SNORD89 mRNACTDPMID:23649840
Snord89Mouseparacetamol increases expressionISOSNORD89 (Homo sapiens)6480464Acetaminophen results in increased expression of SNORD89 mRNACTDPMID:21420995
Snord89MouseS-(1,2-dichlorovinyl)-L-cysteine multiple interactionsISOSNORD89 (Homo sapiens)6480464[S-(1 and 2-dichlorovinyl)cysteine affects the susceptibility to Lipopolysaccharides] which results in increased expression of SNORD89 mRNACTDPMID:35811015
Snord89Mousetrichostatin A increases expressionISOSNORD89 (Homo sapiens)6480464trichostatin A results in increased expression of SNORD89 mRNACTDPMID:24935251
Snord89Mousetrovafloxacin increases expressionEXP 6480464trovafloxacin results in increased expression of SNORD89 mRNACTDPMID:35537566
Snord89Mouseversicolorin A increases expressionISOSNORD89 (Homo sapiens)6480464versicolorin A results in increased expression of SNORD89 mRNACTDPMID:32106047

1 to 15 of 15 rows

Biological Process

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Snord89Mousebiological_process involved_inND 2290270 MGIGO_REF:0000015

Cellular Component

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Snord89Mousecellular_component is_active_inND 2290270 MGIGO_REF:0000015

Molecular Function

  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
Snord89Mousemolecular_function enablesND 2290270 MGIGO_REF:0000015


#
Reference Title
Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
PMID:11387227   PMID:11424213  



Snord89
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39139,587,828 - 39,587,921 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl139,587,826 - 39,587,935 (-)EnsemblGRCm39 Ensembl
GRCm38139,548,747 - 39,548,840 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl139,548,745 - 39,548,854 (-)EnsemblGRCm38mm10GRCm38
MGSCv37139,605,592 - 39,605,685 (-)NCBIGRCm37MGSCv37mm9NCBIm37
Celera139,343,294 - 39,343,387 (-)NCBICelera
Cytogenetic Map1BNCBI
cM Map118.32NCBI
SNORD89
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382101,272,936 - 101,273,049 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2101,272,936 - 101,273,049 (-)EnsemblGRCh38hg38GRCh38
GRCh372101,889,398 - 101,889,511 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362101,255,830 - 101,255,943 (-)NCBINCBI36Build 36hg18NCBI36
Celera296,093,386 - 96,093,499 (-)NCBICelera
Cytogenetic Map2q11.2NCBI
HuRef295,653,585 - 95,653,698 (-)NCBIHuRef
CHM1_12101,893,785 - 101,893,898 (-)NCBICHM1_1
T2T-CHM13v2.02101,731,639 - 101,731,752 (-)NCBIT2T-CHM13v2.0
Snord89
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8949,323,671 - 49,323,785 (-)NCBIGRCr8
mRatBN7.2941,827,972 - 41,828,086 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl941,827,972 - 41,828,086 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl946,283,274 - 46,283,388 (-)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map9q22NCBI
LOC119873789
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha1041,574,657 - 41,574,771 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01042,517,431 - 42,517,545 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1042,517,431 - 42,517,545 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11042,229,949 - 42,230,063 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01042,512,699 - 42,512,813 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01042,704,109 - 42,704,223 (+)NCBIUU_Cfam_GSD_1.0

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Variants in Snord89
2 total Variants

1 to 10 of 349 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670405)x3 copy number gain See cases [RCV000050445] Chr21:7749532..46670405 [GRCh38]
Chr21:15499847..48090317 [GRCh37]
Chr21:14421718..46914745 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic|conflicting interpretations of pathogenicity|conflicting data from submitters
GRCh38/hg38 21q22.11(chr21:31339386-32311519)x1 copy number loss See cases [RCV000052805] Chr21:31339386..32311519 [GRCh38]
Chr21:32711701..33683830 [GRCh37]
Chr21:31633572..32605701 [NCBI36]
Chr21:21q22.11		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46623792)x3 copy number gain See cases [RCV000053042] Chr21:7749532..46623792 [GRCh38]
Chr21:14595524..48043704 [GRCh37]
Chr21:13517395..46868132 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46653090)x3 copy number gain See cases [RCV000053040] Chr21:7749532..46653090 [GRCh38]
Chr21:14539679..48073002 [GRCh37]
Chr21:13461550..46897430 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46623792)x3 copy number gain See cases [RCV000053043] Chr21:7749532..46623792 [GRCh38]
Chr21:14629063..48043704 [GRCh37]
Chr21:13550934..46868132 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670546)x3 copy number gain See cases [RCV000053045] Chr21:7749532..46670546 [GRCh38]
Chr21:15499647..48090458 [GRCh37]
Chr21:14421518..46914886 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46661140)x3 copy number gain See cases [RCV000053065] Chr21:7749532..46661140 [GRCh38]
Chr21:15499647..48081052 [GRCh37]
Chr21:14421518..46905480 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46661140)x3 copy number gain See cases [RCV000053067] Chr21:7749532..46661140 [GRCh38]
Chr21:15499847..48081052 [GRCh37]
Chr21:14421718..46905480 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46670405)x3 copy number gain See cases [RCV000053068] Chr21:7749532..46670405 [GRCh38]
Chr21:20655360..48090317 [GRCh37]
Chr21:19577231..46914745 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
GRCh38/hg38 21p11.2-q22.3(chr21:7749532-46623792)x3 copy number gain See cases [RCV000053039] Chr21:7749532..46623792 [GRCh38]
Chr21:14524963..48043704 [GRCh37]
Chr21:13446834..46868132 [NCBI36]
Chr21:21p11.2-q22.3		 pathogenic
1 to 10 of 349 rows

Predicted Target Of
Summary Value
Count of predictions:297
Count of miRNA genes:270
Interacting mature miRNAs:287
Transcripts:ENSMUST00000104516
Prediction methods:Microtar, Miranda, Rnahybrid
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 23 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
11039528Ccc3_mcolitis susceptibility in the Collaborative Cross 3 (mouse)13680142195051546Mouse
1301011Cplaq4_mcircadian period of locomotor activity 4 (mouse)Not determined1967344243673601Mouse
1357524W6q14_mweight 6 weeks QTL 14 (mouse)Not determined13476013873976915Mouse
1301073Orch5_mautoimmune orchitis resistance 5 (mouse)Not determined11906535153065454Mouse
1357488Splq3_mspleen weight QTL 3 (mouse)Not determined134760138150193871Mouse
1357651Lgq5_mlate growth QTL 5 (mouse)Not determined13476013873976915Mouse
11100001Col4a1m1_mcollagen, type IV, alpha 1 modifier 1 (mouse)12555019162946882Mouse
13824984Twq5_mtestis weight QTL 5 (mouse)13069992184732197Mouse
1301240Sluc15_msusceptibility to lung cancer 15 (mouse)Not determined11906535153065454Mouse
1357759W3q12_mweight 3 weeks QTL 12 (mouse)Not determined13476013873976915Mouse

1 to 10 of 23 rows






Ensembl Acc Id: ENSMUST00000104516
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl139,587,826 - 39,587,935 (-)Ensembl
GRCm38.p6 Ensembl139,548,745 - 39,548,854 (-)Ensembl
RefSeq Acc Id: NR_028555
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39139,587,828 - 39,587,921 (-)NCBI
GRCm38139,548,747 - 39,548,840 (-)ENTREZGENE
MGSCv37139,605,592 - 39,605,685 (-)RGD
Celera139,343,294 - 39,343,387 (-)RGD
cM Map1 ENTREZGENE
Sequence:
RGD ID:6873534
Promoter ID:EPDNEW_M218
Type:single initiation site
Name:Snord89_1
Description:Mus musculus small nucleolar RNA, C/D box 89 , 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
GRCm38139,548,850 - 39,548,910EPDNEW


Database
Acc Id
Source(s)
Ensembl Genes ENSMUSG00000077704 Ensembl, ENTREZGENE
Ensembl Transcript ENSMUST00000104516 ENTREZGENE
MGD MGI:3819562 ENTREZGENE
NCBI Gene 100217461 ENTREZGENE
PhenoGen Snord89 PhenoGen
RNAcentral URS000069EC6D RNACentral
  URS000075A30E RNACentral