SNORD38C (small nucleolar RNA, C/D box 38C) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: SNORD38C (small nucleolar RNA, C/D box 38C) Homo sapiens
Analyze
Symbol: SNORD38C
Name: small nucleolar RNA, C/D box 38C
RGD ID: 12738311
HGNC Page HGNC:52227
Description: Predicted to be involved in RNA processing. Predicted to be located in nucleolus.
Type: snorna
RefSeq Status: PROVISIONAL
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
GRCh38353,333,061 - 53,333,127 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl353,333,060 - 53,333,128 (-)EnsemblGRCh38hg38GRCh38
GRCh37353,367,088 - 53,367,154 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3p21.1NCBI
T2T-CHM13v2.0353,366,044 - 53,366,110 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleolus  (IEA)

References
Additional References at PubMed
PMID:27174936  


Genomics

Comparative Map Data
SNORD38C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38353,333,061 - 53,333,127 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl353,333,060 - 53,333,128 (-)EnsemblGRCh38hg38GRCh38
GRCh37353,367,088 - 53,367,154 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3p21.1NCBI
T2T-CHM13v2.0353,366,044 - 53,366,110 (-)NCBIT2T-CHM13v2.0
Gm23615
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X72,853,023 - 72,853,087 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX72,853,023 - 72,853,087 (+)EnsemblGRCm39 Ensembl
GRCm38X73,809,417 - 73,809,481 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX73,809,417 - 73,809,481 (+)EnsemblGRCm38mm10GRCm38
Cytogenetic MapXA7.3NCBI


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p21.31-14.3(chr3:49461000-55314500)x1 copy number loss See cases [RCV000051511] Chr3:49461000..55314500 [GRCh38]
Chr3:49498433..55348528 [GRCh37]
Chr3:49473437..55323568 [NCBI36]
Chr3:3p21.31-14.3		 pathogenic
GRCh38/hg38 3p21.1-14.3(chr3:53287477-57025368)x1 copy number loss See cases [RCV000053929] Chr3:53287477..57025368 [GRCh38]
Chr3:53321495..57059396 [GRCh37]
Chr3:53296535..57034436 [NCBI36]
Chr3:3p21.1-14.3		 uncertain significance
GRCh38/hg38 3p21.2-14.3(chr3:51394434-55064449)x1 copy number loss See cases [RCV000143631] Chr3:51394434..55064449 [GRCh38]
Chr3:51431865..55098476 [GRCh37]
Chr3:51406905..55073516 [NCBI36]
Chr3:3p21.2-14.3		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:67
Interacting mature miRNAs:67
Transcripts:ENST00000384381
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 3 13 1 3
Low 41 22 41 20 165 23 59 29 56 40 65 41 3 8 3
Below cutoff 6 6 3 3 5 3 7 8 10 7 9 14 1 4

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000384381
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl353,333,060 - 53,333,128 (-)Ensembl
RefSeq Acc Id: NR_145715
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38353,333,061 - 53,333,127 (-)NCBI
T2T-CHM13v2.0353,366,044 - 53,366,110 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SNORD38C COSMIC
Ensembl Genes ENSG00000207109 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000384381 ENTREZGENE
GTEx ENSG00000207109 GTEx
HGNC ID HGNC:52227 ENTREZGENE
Human Proteome Map SNORD38C Human Proteome Map
NCBI Gene SNORD38C ENTREZGENE
RNAcentral URS0000ABD8BE RNACentral