SNORD29 (small nucleolar RNA, C/D box 29) - Rat Genome Database

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Gene: SNORD29 (small nucleolar RNA, C/D box 29) Homo sapiens
Analyze
Symbol: SNORD29
Name: small nucleolar RNA, C/D box 29
RGD ID: 1346054
HGNC Page HGNC:10151
Description: Predicted to be involved in RNA processing. Predicted to be located in nucleolus; INTERACTS WITH aflatoxin B1; sodium arsenite; versicolorin A.
Type: snorna
RefSeq Status: VALIDATED
Previously known as: RNU29; U29
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381162,853,904 - 62,853,968 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371162,621,376 - 62,621,440 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361162,377,952 - 62,378,016 (-)NCBINCBI36Build 36hg18NCBI36
Celera1159,944,772 - 59,944,836 (-)NCBICelera
Cytogenetic Map11q12.3NCBI
HuRef1158,950,413 - 58,950,477 (-)NCBIHuRef
CHM1_11162,504,396 - 62,504,460 (-)NCBICHM1_1
T2T-CHM13v2.01162,843,299 - 62,843,363 (-)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. 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:27609421  


Genomics


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(chr11:62314663-62788240)x3 copy number gain not provided [RCV000849841] Chr11:62314663..62788240 [GRCh37]
Chr11:11q12.3		 uncertain significance
GRCh37/hg19 11q12.3(chr11:62487052-62788240)x3 copy number gain not provided [RCV000846292] Chr11:62487052..62788240 [GRCh37]
Chr11:11q12.3		 uncertain significance
Single allele deletion Intellectual disability [RCV001293382] Chr11:118359328..118372573 [GRCh37]
Chr11:11p15.3-q23.3		 pathogenic
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
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:166
Count of miRNA genes:160
Interacting mature miRNAs:166
Transcripts:ENST00000383926
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


Sequence


Reference Sequences
RefSeq Acc Id: NR_002559
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381162,853,904 - 62,853,968 (-)NCBI
GRCh371162,621,376 - 62,621,440 (-)RGD
Build 361162,377,952 - 62,378,016 (-)NCBI Archive
Celera1159,944,772 - 59,944,836 (-)RGD
HuRef1158,950,413 - 58,950,477 (-)RGD
CHM1_11162,504,396 - 62,504,460 (-)NCBI
T2T-CHM13v2.01162,843,299 - 62,843,363 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SNORD29 COSMIC
GTEx SNORD29 GTEx
HGNC ID HGNC:10151 ENTREZGENE
Human Proteome Map SNORD29 Human Proteome Map
NCBI Gene 9297 ENTREZGENE
OMIM 603228 OMIM
PharmGKB PA34517 PharmGKB
RNAcentral URS0000164B86 RNACentral