Snord49a (small nucleolar RNA, C/D box 49A) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Snord49a (small nucleolar RNA, C/D box 49A) Mus musculus
Analyze
Symbol: Snord49a
Name: small nucleolar RNA, C/D box 49A
RGD ID: 2302603
MGI Page MGI
Description: INTERACTS WITH aldehydo-D-glucose; buta-1,3-diene; D-glucose
Type: snorna
RefSeq Status: PROVISIONAL
Previously known as: MBII-2; MBII-243
RGD Orthologs
Human
Rat
Dog
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391162,494,286 - 62,494,347 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1162,494,276 - 62,494,347 (+)EnsemblGRCm39 Ensembl
GRCm381162,603,460 - 62,603,521 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1162,603,450 - 62,603,521 (+)EnsemblGRCm38mm10GRCm38
MGSCv371162,416,962 - 62,417,023 (+)NCBIGRCm37MGSCv37mm9NCBIm37
Celera1169,523,089 - 69,523,150 (+)NCBICelera
Cytogenetic Map11B2NCBI
cM Map1138.51NCBI
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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11387227   PMID:11424213  


Genomics

Comparative Map Data
Snord49a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391162,494,286 - 62,494,347 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1162,494,276 - 62,494,347 (+)EnsemblGRCm39 Ensembl
GRCm381162,603,460 - 62,603,521 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1162,603,450 - 62,603,521 (+)EnsemblGRCm38mm10GRCm38
MGSCv371162,416,962 - 62,417,023 (+)NCBIGRCm37MGSCv37mm9NCBIm37
Celera1169,523,089 - 69,523,150 (+)NCBICelera
Cytogenetic Map11B2NCBI
cM Map1138.51NCBI
SNORD49A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381716,440,036 - 16,440,106 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1716,440,036 - 16,440,106 (+)EnsemblGRCh38hg38GRCh38
GRCh371716,343,350 - 16,343,420 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361716,284,075 - 16,284,145 (+)NCBINCBI36Build 36hg18NCBI36
Build 341716,284,074 - 16,284,145NCBI
Celera1716,246,249 - 16,246,319 (+)NCBICelera
Cytogenetic Map17p11.2NCBI
HuRef1716,209,814 - 16,209,884 (+)NCBIHuRef
CHM1_11716,352,958 - 16,353,028 (+)NCBICHM1_1
T2T-CHM13v2.01716,342,339 - 16,342,409 (+)NCBIT2T-CHM13v2.0
Snord49a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81047,796,770 - 47,796,841 (+)NCBIGRCr8
mRatBN7.21047,297,488 - 47,297,559 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1047,297,488 - 47,297,559 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl1048,928,263 - 48,928,334 (+)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map10q23NCBI
LOC119872054
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha539,634,123 - 39,634,193 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0539,597,912 - 39,597,982 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1539,569,897 - 39,569,967 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0539,515,161 - 39,515,231 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0539,707,326 - 39,707,396 (-)NCBIUU_Cfam_GSD_1.0

Variants

.
Variants in Snord49a
1 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:138
Count of miRNA genes:128
Interacting mature miRNAs:138
Transcripts:ENSMUST00000083800
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
26884446Sklq10_mskull length QTL 10, 10 week (mouse)11325000062890826Mouse
26884453Sklq16_mskull length QTL 16, 16 week (mouse)11325000072690826Mouse
13208559Wght10_mweight 10 (mouse)11395000088890826Mouse
13208558Lgth12_mbody length 12 (mouse)11395000094890826Mouse
1300905Scc6_mcolon tumor susceptibility 6 (mouse)Not determined11688027789019734Mouse
26884401Huml4_mhumerus length 4, 10 week (mouse)111155000068490826Mouse
27226762Feml21_mfemur length 21, 16 week (mouse)111175000065990826Mouse
1357640Orq2_movulation rate QTL 2 (mouse)Not determined111226863768500330Mouse
4141127W3q4_mweight 3 weeks QTL 4 (mouse)Not determined1226863768500330Mouse
4141470Egq4_mearly growth QTL 4 (mouse)Not determined1226863768500330Mouse
4142109W10q2_mweight 10 weeks QTL 2 (mouse)Not determined1226863768500330Mouse
4141582Lgaq1_mlate growth adjusted QTL 1 (mouse)Not determined1226863768500330Mouse
4142308W6q3_mweight 6 weeks QTL 3 (mouse)Not determined111226863768500330Mouse
4142216Lgq1_mlate growth QTL 1 (mouse)Not determined1226863768500330Mouse
4141966Tailq1_mtail length QTL 1 (mouse)Not determined1226863768500330Mouse
1357851Scfq3_msubcutaneous fat pad weight QTL 3 (mouse)Not determined111226863768500330Mouse
1357720Kidpq1_mkidney weight percentage QTL 1 (mouse)Not determined111226863768500330Mouse
1357437Epfq4_mepididymal fat pad weight QTL 4 (mouse)Not determined111226863768500330Mouse
1559002Lmrq4_mLeishmania major resistance QTL 4 (mouse)Not determined111226863769684947Mouse
39128214Lwq20_mliver weight QTL 20 (mouse)1112268637118022724Mouse
1558945Orgwq8_morgan weight QTL 8 (mouse)Not determined111705617567078411Mouse
10053687Eae6_msusceptibility to experimental allergic encephalomyelitis 6 (mouse)Not determined111778196668500330Mouse
4141894Nidd6k_mNidd6 on KK-A (mouse)Not determined1912420496897826Mouse
10412246Dfs2_mdental fluorosis suseptibility 2 (mouse)Not determined112180736495881231Mouse
13524848Ppiq7_mprepulse inhibition QTL 7 (mouse)112856914762569147Mouse
1301426Desp2_mdespair 2 (mouse)Not determined112870858162708700Mouse
11522752Cocia18_mcocaine-induced activity, QTL 18 (mouse)113100820965008209Mouse
11059563Lmr31_mleishmaniasis resistance 31 (mouse)113210057766100694Mouse
1357782Char8_mP. chabaudi malaria resistance QTL 8 (mouse)Not determined113557861669684987Mouse
13208569Bmiq10_mbody mass index QTL 10 (mouse)113589082784890826Mouse
1301328Mol4_mmodifier of LPS-response 4 (mouse)Not determined113628257783481356Mouse
1301788Lbw8_mlupus NZB x NZW 8 (mouse)Not determined113650328770509492Mouse
1301896Tria1_mT-cell receptor induced activation 1 (mouse)Not determined113661356570613855Mouse
4141853Skmw17_mskeletal muscle weight 17 (mouse)Not determined113708094171081064Mouse
10766457Nwa3_mNew Zealand White autoimmunity 3 (mouse)113801611572016209Mouse
11532698Sluc36a_msusceptibility to lung cancer 36a (mouse)114225661776256730Mouse
11532699Sluc36b_msusceptibility to lung cancer 36b (mouse)114225661776256730Mouse
4142300Ctrq3_mC. trachomatis resistance QTL 3 (mouse)Not determined114463003876854757Mouse
4141367Inf1_macute ozone induced inflammation (mouse)Not determined44630038113058009Mouse
1302021Nidd1n_mnon-insulin-dependent diabetes mellitus 1 in NSY (mouse)Not determined114516587379978324Mouse
1357878Mastr_mmodifier of astrocytoma (mouse)Not determined114570858189818733Mouse
1300765Bbaa4_mB.burgdorferi-associated arthritis 4 (mouse)Not determined114618516780185262Mouse
1301988Bmd11_mbone mineral density 11 (mouse)Not determined114631940780319522Mouse
1301830Ssta4_msusceptibility to Salmonella typhimurium antigens 4 (mouse)Not determined115007819184078411Mouse
13524840Ppiq9a_mprepulse inhibition QTL 9a (mouse)115249438586494385Mouse
1300774Pgia7_mproteoglycan induced arthritis 7 (mouse)Not determined115339058887390737Mouse
4141084Spqq1_msperm quality QTL 1 (mouse)Not determined5406567063319522Mouse
1302186Blmpf2_mbleomycin-induced pulmonary fibrosis 2 (mouse)Not determined115406567067078411Mouse
4142148Ckdbp2_mchronic kidney disease blood pressure locus 2 (mouse)Not determined115408094165103841Mouse
4141830Pregq1_mpregnancy QTL 1 (mouse)Not determined115412675283733652Mouse
4141875Etax9_methanol induced ataxia 9 (mouse)Not determined5528498572209927Mouse
4142121Tmc1m2_mTmc1 modifier 2 (mouse)Not determined1156864027114157957Mouse
1300664Etohcta9_methanol conditioned taste aversion 9 (mouse)Not determined115775466091754758Mouse
10053682Eae45_mexperimental allergic encephalomyelitis susceptibility 45 (mouse)Not determined115849055574754758Mouse
1300924Ity2_mimmunity to S. typhimurium 2 (mouse)Not determined15850803087695238Mouse
4141982Skts-fp2_mskin tumor susceptibility in FVB and PWK 2 (mouse)Not determined5871926685066529Mouse
11532697Sluc36_msusceptibility to lung cancer 36 (mouse)115925661769482699Mouse
1301987Pid3_mprior incubation determinant 3 (mouse)Not determined116168682088699728Mouse
1301319Dautb4_mdopamine uptake transporter binding 4 (mouse)Not determined116215600596156153Mouse


Expression


Sequence


RefSeq Acc Id: ENSMUST00000083800
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1162,494,276 - 62,494,347 (+)Ensembl
GRCm38.p6 Ensembl1162,603,450 - 62,603,521 (+)Ensembl
RefSeq Acc Id: NR_028550
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391162,494,286 - 62,494,347 (+)NCBI
GRCm381162,603,460 - 62,603,521 (+)ENTREZGENE
MGSCv371162,416,962 - 62,417,023 (+)RGD
Celera1169,523,089 - 69,523,150 (+)RGD
cM Map11 ENTREZGENE
Sequence:
Promoters
RGD ID:8674992
Promoter ID:EPDNEW_M15527
Type:single initiation site
Name:Snord49a_1
Description:Mus musculus small nucleolar RNA, C/D box 49A , 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
GRCm381162,603,452 - 62,603,512EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSMUSG00000065734 Ensembl, ENTREZGENE
Ensembl Transcript ENSMUST00000083800 ENTREZGENE
MGD MGI:3819538 ENTREZGENE
NCBI Gene 100217455 ENTREZGENE
PhenoGen Snord49a PhenoGen
RNAcentral URS000033D40A RNACentral