Snhg15 (small nucleolar RNA host gene 15) - Rat Genome Database

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Gene: Snhg15 (small nucleolar RNA host gene 15) Mus musculus
Analyze
Symbol: Snhg15
Name: small nucleolar RNA host gene 15
RGD ID: 2294157
MGI Page MGI
Description: Acts upstream of or within several processes, including mitotic sister chromatid segregation; satellite cell activation involved in skeletal muscle regeneration; and skeletal muscle satellite cell proliferation. Located in cytoplasm. Orthologous to human SNHG15 (small nucleolar RNA host gene 15).
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: Gm11974; predicted gene 11974; S; SAM
RGD Orthologs
Human
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,475,591 - 6,478,760 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl116,475,295 - 6,478,841 (-)EnsemblGRCm39 Ensembl
GRCm38116,525,591 - 6,528,760 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,525,591 - 6,528,779 (-)EnsemblGRCm38mm10GRCm38
MGSCv37116,425,594 - 6,428,763 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36116,425,594 - 6,428,965 (-)NCBIMGSCv36mm8
Celera117,012,670 - 7,015,839 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map114.37NCBI
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
cytoplasm  (IDA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
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:10349636   PMID:10512203   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12904583   PMID:14610273   PMID:15741177   PMID:15840001   PMID:16141072   PMID:16141073  
PMID:27899360   PMID:32483152   PMID:32862188   PMID:32970504   PMID:33572758   PMID:34338972   PMID:34453220   PMID:35791576  


Genomics

Comparative Map Data
Snhg15
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39116,475,591 - 6,478,760 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl116,475,295 - 6,478,841 (-)EnsemblGRCm39 Ensembl
GRCm38116,525,591 - 6,528,760 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl116,525,591 - 6,528,779 (-)EnsemblGRCm38mm10GRCm38
MGSCv37116,425,594 - 6,428,763 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36116,425,594 - 6,428,965 (-)NCBIMGSCv36mm8
Celera117,012,670 - 7,015,839 (-)NCBICelera
Cytogenetic Map11A1NCBI
cM Map114.37NCBI
SNHG15
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38744,983,023 - 44,986,696 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl744,983,019 - 44,986,961 (-)EnsemblGRCh38hg38GRCh38
GRCh37745,022,622 - 45,026,295 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36744,989,152 - 44,992,784 (-)NCBINCBI36Build 36hg18NCBI36
Celera745,121,376 - 45,125,025 (-)NCBICelera
Cytogenetic Map7p13NCBI
HuRef744,907,793 - 44,911,442 (-)NCBIHuRef
CHM1_1745,026,541 - 45,030,190 (-)NCBICHM1_1
T2T-CHM13v2.0745,143,371 - 45,147,061 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2745,062,083 - 45,065,732 (-)NCBI

Variants

.
Variants in Snhg15
70 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:407
Count of miRNA genes:209
Interacting mature miRNAs:217
Transcripts:ENSMUST00000124818, ENSMUST00000129570, ENSMUST00000134527, ENSMUST00000147762
Prediction methods: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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357722Vtbt11_mvertebral trabecular bone trait 11 (mouse)Not determined11123880487Mouse
1300768Tshp9_mtooth shape 9 (mouse)Not determined11125976374Mouse
1301765Skull15_mskull morphology 15 (mouse)Not determined11125976374Mouse
1300661Lmr6_mleishmaniasis resistance 6 (mouse)Not determined11125976374Mouse
10044008Hbnr15_mHeligmosomoides bakeri nematode resistance 15 (mouse)Not determined1122705234227232Mouse
1300599Cocrb11_mcocaine related behavior 11 (mouse)Not determined11267035536671472Mouse
27095914Pglq16_mpelvic girdle length QTL 16, 16 week (mouse)11325000018150000Mouse
27095919Pglq10_mpelvic girdle length QTL 10, 10 week (mouse)11325000018450000Mouse
27095925Pglq5_mpelvic girdle length QTL 5, 5 week (mouse)11325000019750000Mouse
27095904Scvln12_msacral vertebrae length 2, 10 week (mouse)11325000034495048Mouse
27095909Scvln6_msacral vertebrae length 2, 5 week (mouse)11325000044090827Mouse
27226798Scvln18_msacral vertebrae length 2, 16 week (mouse)11325000060690826Mouse
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
10053676Eae44a_mexperimental allergic encephalomyelitis susceptibility 44a (mouse)Not determined11450789621379532Mouse
27226741Metcl5_mmetatarsal-calcaneal length 5, 5 week (mouse)11465000046290827Mouse
27226735Metcl16_mmetatarsal-calcaneal length 16, 16 week (mouse)11525000035090827Mouse


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000124818
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,475,585 - 6,478,820 (-)Ensembl
GRCm38.p6 Ensembl116,525,591 - 6,528,766 (-)Ensembl
RefSeq Acc Id: ENSMUST00000129570
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,475,591 - 6,478,766 (-)Ensembl
GRCm38.p6 Ensembl116,525,592 - 6,527,759 (-)Ensembl
RefSeq Acc Id: ENSMUST00000134527
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,477,051 - 6,478,763 (-)Ensembl
GRCm38.p6 Ensembl116,527,051 - 6,528,763 (-)Ensembl
RefSeq Acc Id: ENSMUST00000147762
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,475,295 - 6,478,841 (-)Ensembl
GRCm38.p6 Ensembl116,525,591 - 6,528,779 (-)Ensembl
RefSeq Acc Id: ENSMUST00000241845
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,475,591 - 6,478,766 (-)Ensembl
RefSeq Acc Id: ENSMUST00000242258
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,478,030 - 6,478,472 (-)Ensembl
RefSeq Acc Id: ENSMUST00000245113
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,475,593 - 6,478,727 (-)Ensembl
RefSeq Acc Id: ENSMUST00000245397
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,475,591 - 6,478,768 (-)Ensembl
RefSeq Acc Id: ENSMUST00000246248
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl116,478,028 - 6,478,818 (-)Ensembl
RefSeq Acc Id: NR_045893
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39116,475,591 - 6,478,760 (-)NCBI
GRCm38116,525,591 - 6,528,760 (-)ENTREZGENE
Celera117,012,670 - 7,015,839 (-)ENTREZGENE
cM Map11 ENTREZGENE
Sequence:
Promoters
RGD ID:6820796
Promoter ID:MM_KWN:6372
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:AK160548_GM11974,   ENSMUST00000082579,   OTTMUST00000011445,   OTTMUST00000011447
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36116,428,286 - 6,428,786 (-)MPROMDB
RGD ID:8673908
Promoter ID:EPDNEW_M14985
Type:initiation region
Name:Snhg15_2
Description:Mus musculus small nucleolar RNA host gene 15 , long non-codingRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M14986  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38116,528,456 - 6,528,516EPDNEW
RGD ID:15093876
Promoter ID:EPDNEWNC_M1789
Type:multiple initiation site
Name:Snhg15_1
Description:small nucleolar RNA host gene 15 [Source:MGISymbol;Acc:MGI:3650059]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38116,528,750 - 6,528,810EPDNEWNC
RGD ID:8673912
Promoter ID:EPDNEW_M14986
Type:initiation region
Name:Snhg15_1
Description:Mus musculus small nucleolar RNA host gene 15 , long non-codingRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M14985  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38116,528,750 - 6,528,810EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3650059 AgrOrtholog
Ensembl Genes ENSMUSG00000085156 Ensembl, ENTREZGENE
Ensembl Transcript ENSMUST00000245113 ENTREZGENE
MGD MGI:3650059 ENTREZGENE
NCBI Gene 100041286 ENTREZGENE
PhenoGen Snhg15 PhenoGen
RNAcentral URS000075C6F7 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-28 Snhg15  small nucleolar RNA host gene 15  Gm11974  predicted gene 11974  Symbol and/or name change 5135510 APPROVED
2012-01-17 Gm11974  predicted gene 11974  OTTMUSG00000005115  predicted gene, OTTMUSG00000005115  Symbol and/or name change 5135510 APPROVED