SNORD15A (small nucleolar RNA, C/D box 15A) - Rat Genome Database

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Gene: SNORD15A (small nucleolar RNA, C/D box 15A) Homo sapiens
Analyze
Symbol: SNORD15A
Name: small nucleolar RNA, C/D box 15A
RGD ID: 1343552
HGNC Page HGNC:10114
Description: Predicted to be involved in RNA processing. Predicted to be located in nucleolus; INTERACTS WITH (-)-epigallocatechin 3-gallate; 2,3,7,8-tetrachlorodibenzodioxine; cisplatin.
Type: snorna
RefSeq Status: VALIDATED
Previously known as: RNU15A; SNORNA; U15A
RGD Orthologs
Mouse
Rat
Dog
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381175,400,391 - 75,400,538 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1175,400,391 - 75,400,538 (+)EnsemblGRCh38hg38GRCh38
GRCh371175,111,435 - 75,111,582 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361174,789,083 - 74,789,230 (+)NCBINCBI36Build 36hg18NCBI36
Celera1172,419,186 - 72,419,333 (+)NCBICelera
Cytogenetic Map11q13.4NCBI
HuRef1171,408,871 - 71,409,018 (+)NCBIHuRef
CHM1_11174,995,010 - 74,995,157 (+)NCBICHM1_1
T2T-CHM13v2.01175,329,979 - 75,330,126 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleolus  (IEA)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
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:7789996   PMID:8319909   PMID:19446021   PMID:29117863   PMID:34411703  


Genomics

Comparative Map Data
SNORD15A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381175,400,391 - 75,400,538 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1175,400,391 - 75,400,538 (+)EnsemblGRCh38hg38GRCh38
GRCh371175,111,435 - 75,111,582 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361174,789,083 - 74,789,230 (+)NCBINCBI36Build 36hg18NCBI36
Celera1172,419,186 - 72,419,333 (+)NCBICelera
Cytogenetic Map11q13.4NCBI
HuRef1171,408,871 - 71,409,018 (+)NCBIHuRef
CHM1_11174,995,010 - 74,995,157 (+)NCBICHM1_1
T2T-CHM13v2.01175,329,979 - 75,330,126 (+)NCBIT2T-CHM13v2.0
Snord15a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39799,131,992 - 99,132,139 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl799,131,992 - 99,132,139 (-)EnsemblGRCm39 Ensembl
GRCm38799,482,785 - 99,482,932 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl799,482,785 - 99,482,932 (-)EnsemblGRCm38mm10GRCm38
MGSCv377106,631,295 - 106,631,442 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36799,356,868 - 99,357,015 (-)NCBIMGSCv36mm8
Celera799,807,770 - 99,807,917 (-)NCBICelera
Cytogenetic Map7E1NCBI
cM Map754.08NCBI
Snord15a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81163,194,901 - 163,195,048 (-)NCBIGRCr8
mRatBN7.21153,782,788 - 153,782,935 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1153,782,788 - 153,782,935 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl1164,440,292 - 164,440,439 (-)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map1q32NCBI
LOC119865100
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha2122,951,461 - 22,951,608 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02123,388,720 - 23,388,867 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2123,388,720 - 23,388,867 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12123,187,053 - 23,187,200 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02123,383,348 - 23,383,495 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02123,301,275 - 23,301,422 (-)NCBIUU_Cfam_GSD_1.0


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q13.4-14.1(chr11:71923251-79662025)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052684]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052684]|See cases [RCV000052684] Chr11:71923251..79662025 [GRCh38]
Chr11:71634297..79373069 [GRCh37]
Chr11:71311945..79050717 [NCBI36]
Chr11:11q13.4-14.1		 pathogenic
GRCh38/hg38 11q13.4-13.5(chr11:71928796-77064521)x1 copy number loss See cases [RCV000052708] Chr11:71928796..77064521 [GRCh38]
Chr11:71639842..76751808 [GRCh37]
Chr11:71317490..76453216 [NCBI36]
Chr11:11q13.4-13.5		 pathogenic
GRCh38/hg38 11q13.4-14.1(chr11:71969881-78232895)x1 copy number loss See cases [RCV000052709] Chr11:71969881..78232895 [GRCh38]
Chr11:71680927..77943941 [GRCh37]
Chr11:71358575..77621589 [NCBI36]
Chr11:11q13.4-14.1		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470) copy number gain See cases [RCV000511729] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:230616-134938470)x3 copy number gain See cases [RCV000510881] Chr11:230616..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11q13.4-23.3(chr11:71588805-116680918)x3 copy number gain not provided [RCV000683374] Chr11:71588805..116680918 [GRCh37]
Chr11:11q13.4-23.3		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:198510-134934063)x3 copy number gain not provided [RCV000737348] Chr11:198510..134934063 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
GRCh37/hg19 11p15.5-q25(chr11:70864-134938470)x3 copy number gain not provided [RCV000749874] Chr11:70864..134938470 [GRCh37]
Chr11:11p15.5-q25		 pathogenic
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3		 pathogenic
GRCh37/hg19 11q13.4-13.5(chr11:74839014-75366449) copy number gain not specified [RCV002052937] Chr11:74839014..75366449 [GRCh37]
Chr11:11q13.4-13.5		 uncertain significance
NC_000011.9:g.(?_71146421)_(75283128_?)dup duplication 3-methylglutaconic aciduria, type VIIB [RCV003122786] Chr11:71146421..75283128 [GRCh37]
Chr11:11q13.4-13.5		 uncertain significance
GRCh37/hg19 11p13-q25(chr11:32799481-134938470)x3 copy number gain MISSED ABORTION [RCV002282973] Chr11:32799481..134938470 [GRCh37]
Chr11:11p13-q25		 pathogenic
GRCh37/hg19 11q12.2-13.5(chr11:59923608-76272324)x3 copy number gain not provided [RCV003484842] Chr11:59923608..76272324 [GRCh37]
Chr11:11q12.2-13.5		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:132
Count of miRNA genes:132
Interacting mature miRNAs:132
Transcripts:ENST00000384214
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.


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 sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1 9 4 16 1 3 2
Low 138 3 75 58 287 63 162 56 78 75 164 184 6 1 2 4
Below cutoff 15 34 24 22 24 8 4 10 24 20 45

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000384214
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1175,400,391 - 75,400,538 (+)Ensembl
RefSeq Acc Id: NR_000005
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381175,400,391 - 75,400,538 (+)NCBI
GRCh371175,111,435 - 75,111,582 (+)RGD
Build 361174,789,083 - 74,789,230 (+)NCBI Archive
Celera1172,419,186 - 72,419,333 (+)RGD
HuRef1171,408,871 - 71,409,018 (+)ENTREZGENE
CHM1_11174,995,010 - 74,995,157 (+)NCBI
T2T-CHM13v2.01175,329,979 - 75,330,126 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SNORD15A COSMIC
Ensembl Genes ENSG00000206941 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000384214 ENTREZGENE
GTEx ENSG00000206941 GTEx
HGNC ID HGNC:10114 ENTREZGENE
Human Proteome Map SNORD15A Human Proteome Map
NCBI Gene 6079 ENTREZGENE
OMIM 600455 OMIM
PharmGKB PA34479 PharmGKB
RNAcentral URS00003A9200 RNACentral