SNORD25 (small nucleolar RNA, C/D box 25) - Rat Genome Database

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Gene: SNORD25 (small nucleolar RNA, C/D box 25) Homo sapiens
Analyze
Symbol: SNORD25
Name: small nucleolar RNA, C/D box 25
RGD ID: 1346154
HGNC Page HGNC:10147
Description: ASSOCIATED WITH Intellectual disability; intellectual disability; leukocyte adhesion deficiency 3; INTERACTS WITH aflatoxin B1; triclosan; versicolorin A
Type: snorna
RefSeq Status: VALIDATED
Previously known as: RNU25; U25
RGD Orthologs
Mouse
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
GRCh381162,855,565 - 62,855,631 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1162,855,564 - 62,855,632 (-)EnsemblGRCh38hg38GRCh38
GRCh371162,623,037 - 62,623,103 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361162,379,613 - 62,379,679 (-)NCBINCBI36Build 36hg18NCBI36
Celera1159,946,433 - 59,946,499 (-)NCBICelera
Cytogenetic Map11q12.3NCBI
HuRef1158,952,074 - 58,952,140 (-)NCBIHuRef
CHM1_11162,506,057 - 62,506,123 (-)NCBICHM1_1
T2T-CHM13v2.01162,844,960 - 62,845,026 (-)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
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# 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
Additional References at PubMed
PMID:8559254   PMID:9387929   PMID:19446021   PMID:22331267   PMID:27609421   PMID:29117863  


Genomics

Comparative Map Data
SNORD25
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381162,855,565 - 62,855,631 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1162,855,564 - 62,855,632 (-)EnsemblGRCh38hg38GRCh38
GRCh371162,623,037 - 62,623,103 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361162,379,613 - 62,379,679 (-)NCBINCBI36Build 36hg18NCBI36
Celera1159,946,433 - 59,946,499 (-)NCBICelera
Cytogenetic Map11q12.3NCBI
HuRef1158,952,074 - 58,952,140 (-)NCBIHuRef
CHM1_11162,506,057 - 62,506,123 (-)NCBICHM1_1
T2T-CHM13v2.01162,844,960 - 62,845,026 (-)NCBIT2T-CHM13v2.0
Gm25855
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39198,701,357 - 8,701,428 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl198,701,357 - 8,701,428 (+)EnsemblGRCm39 Ensembl
GRCm38198,723,993 - 8,724,064 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl198,723,993 - 8,724,064 (+)EnsemblGRCm38mm10GRCm38
Cytogenetic Map19ANCBI


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q12.3(chr11:62433886-63096003)x3 copy number gain See cases [RCV000053620] Chr11:62433886..63096003 [GRCh38]
Chr11:62201358..62863475 [GRCh37]
Chr11:61957934..62620051 [NCBI36]
Chr11:11q12.3		 pathogenic
GRCh38/hg38 11q12.3(chr11:62452571-62862781)x3 copy number gain See cases [RCV000053621] Chr11:62452571..62862781 [GRCh38]
Chr11:62220043..62630253 [GRCh37]
Chr11:61976619..62386829 [NCBI36]
Chr11:11q12.3		 pathogenic
NM_001012662.2(SLC3A2):c.-1259C>T single nucleotide variant Malignant melanoma [RCV000062319] Chr11:62855011 [GRCh38]
Chr11:62622483 [GRCh37]
Chr11:62379059 [NCBI36]
Chr11:11q12.3		 not provided
GRCh38/hg38 11q12.3(chr11:62249520-62946093)x3 copy number gain See cases [RCV000138411] Chr11:62249520..62946093 [GRCh38]
Chr11:62016992..62713565 [GRCh37]
Chr11:61773568..62470141 [NCBI36]
Chr11:11q12.3		 pathogenic
GRCh37/hg19 11q12.3(chr11:61840997-62987330)x1 copy number loss See cases [RCV000448355] Chr11:61840997..62987330 [GRCh37]
Chr11:11q12.3		 likely 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 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
GRCh37/hg19 11q12.3(chr11:62487052-62788240)x3 copy number gain not provided [RCV000846292] Chr11:62487052..62788240 [GRCh37]
Chr11:11q12.3		 uncertain significance
GRCh37/hg19 11q12.3(chr11:62314663-62788240)x3 copy number gain not provided [RCV000849841] Chr11:62314663..62788240 [GRCh37]
Chr11:11q12.3		 uncertain significance
NC_000011.9:g.(?_59596957)_(68707199_?)dup duplication Familial temporal lobe epilepsy 8 [RCV001372442] Chr11:59596957..68707199 [GRCh37]
Chr11:11q12.1-13.3		 uncertain significance
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3		 pathogenic
NC_000011.9:g.(?_58916346)_(64972349_?)dup duplication Leukocyte adhesion deficiency 3 [RCV003113394]|not provided [RCV003113393] Chr11:58916346..64972349 [GRCh37]
Chr11:11q12.1-13.1		 uncertain significance|no classifications from unflagged records
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
GRCh37/hg19 11q12.1-13.3(chr11:56895955-69295402)x3 copy number gain not specified [RCV003986944] Chr11:56895955..69295402 [GRCh37]
Chr11:11q12.1-13.3		 likely pathogenic
GRCh37/hg19 11p11.12-q13.1(chr11:50398499-63924462)x3 copy number gain not specified [RCV003986918] Chr11:50398499..63924462 [GRCh37]
Chr11:11p11.12-q13.1		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:194
Count of miRNA genes:191
Interacting mature miRNAs:194
Transcripts:ENST00000365607
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.

Markers in Region
AF081279  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371162,622,913 - 62,623,447UniSTSGRCh37
Build 361162,379,489 - 62,380,023RGDNCBI36
Celera1159,946,309 - 59,946,843RGD
Cytogenetic Map11q12.3UniSTS
Cytogenetic Map11q13UniSTS
HuRef1158,951,950 - 58,952,484UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENST00000365607
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1162,855,564 - 62,855,632 (-)Ensembl
RefSeq Acc Id: NR_002565
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381162,855,565 - 62,855,631 (-)NCBI
GRCh371162,623,037 - 62,623,103 (-)RGD
Build 361162,379,613 - 62,379,679 (-)NCBI Archive
Celera1159,946,433 - 59,946,499 (-)RGD
HuRef1158,952,074 - 58,952,140 (-)RGD
CHM1_11162,506,057 - 62,506,123 (-)NCBI
T2T-CHM13v2.01162,844,960 - 62,845,026 (-)NCBI
Sequence:
Promoters
RGD ID:6789540
Promoter ID:HG_KWN:13144
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000365607,   NM_001012661,   NM_001012662,   NM_001012663,   NM_001012664,   NM_002394,   NR_003098,   UC001NVO.1,   UC001NVP.1,   UC001NVQ.1,   UC001NVR.1,   UC001NVS.1,   UC001NVT.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361162,378,686 - 62,380,037 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC SNORD25 COSMIC
Ensembl Genes ENSG00000275043 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000365607 ENTREZGENE
GTEx ENSG00000275043 GTEx
HGNC ID HGNC:10147 ENTREZGENE
Human Proteome Map SNORD25 Human Proteome Map
NCBI Gene 9303 ENTREZGENE
OMIM 603224 OMIM
PharmGKB PA34513 PharmGKB
RNAcentral URS0000454FD5 RNACentral