SNORD78 (small nucleolar RNA, C/D box 78) - Rat Genome Database

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Gene: SNORD78 (small nucleolar RNA, C/D box 78) Homo sapiens
Analyze
Symbol: SNORD78
Name: small nucleolar RNA, C/D box 78
RGD ID: 2291781
HGNC Page HGNC:32738
Description: Predicted to be involved in RNA processing. Predicted to be located in nucleolus; INTERACTS WITH (-)-epigallocatechin 3-gallate; 17beta-estradiol; bisphenol A.
Type: snorna
RefSeq Status: VALIDATED
Previously known as: U78
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381173,865,622 - 173,865,686 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371173,834,760 - 173,834,824 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361172,101,394 - 172,101,447 (-)NCBINCBI36Build 36hg18NCBI36
Celera1146,944,240 - 146,944,293 (-)NCBICelera
Cytogenetic Map1q25.1NCBI
HuRef1145,059,726 - 145,059,779 (-)NCBIHuRef
CHM1_11175,257,212 - 175,257,265 (-)NCBICHM1_1
T2T-CHM13v2.01173,223,741 - 173,223,805 (-)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:9819378   PMID:15556860   PMID:19446021   PMID:27174936  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q24.3-31.1(chr1:171039975-186875957)x3 copy number gain See cases [RCV000134876] Chr1:171039975..186875957 [GRCh38]
Chr1:171009116..186845089 [GRCh37]
Chr1:169275740..185111712 [NCBI36]
Chr1:1q24.3-31.1		 pathogenic
GRCh38/hg38 1q24.2-25.2(chr1:169218236-178075834)x1 copy number loss See cases [RCV000137128] Chr1:169218236..178075834 [GRCh38]
Chr1:169187474..178044969 [GRCh37]
Chr1:167454098..176311592 [NCBI36]
Chr1:1q24.2-25.2		 pathogenic
GRCh38/hg38 1q24.3-31.2(chr1:170929720-191065409)x1 copy number loss See cases [RCV000142369] Chr1:170929720..191065409 [GRCh38]
Chr1:170898861..191034539 [GRCh37]
Chr1:169165485..189301162 [NCBI36]
Chr1:1q24.3-31.2		 pathogenic
GRCh38/hg38 1q23.3-25.1(chr1:163382523-175877022)x1 copy number loss See cases [RCV000143292] Chr1:163382523..175877022 [GRCh38]
Chr1:163352313..175846158 [GRCh37]
Chr1:161618937..174112781 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q24.2-31.1(chr1:170036068-187555148)x1 copy number loss See cases [RCV000143688] Chr1:170036068..187555148 [GRCh38]
Chr1:170005209..187524280 [GRCh37]
Chr1:168271833..185790903 [NCBI36]
Chr1:1q24.2-31.1		 pathogenic
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2		 pathogenic
GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3 copy number gain See cases [RCV000051856] Chr1:164922655..180061589 [GRCh38]
Chr1:164891892..180030724 [GRCh37]
Chr1:163158516..178297347 [NCBI36]
Chr1:1q23.3-25.2		 pathogenic
GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3 copy number gain See cases [RCV000051854] Chr1:157747246..176021247 [GRCh38]
Chr1:157717036..175990383 [GRCh37]
Chr1:155983660..174257006 [NCBI36]
Chr1:1q23.1-25.1		 pathogenic
GRCh38/hg38 1q23.3-25.1(chr1:161740907-173965154)x1 copy number loss See cases [RCV000053914] Chr1:161740907..173965154 [GRCh38]
Chr1:161710697..173934292 [GRCh37]
Chr1:159977321..172200915 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q24.1-25.1(chr1:166762832-175327423)x1 copy number loss See cases [RCV000053917] Chr1:166762832..175327423 [GRCh38]
Chr1:166732069..175296559 [GRCh37]
Chr1:164998693..173563182 [NCBI36]
Chr1:1q24.1-25.1		 pathogenic
GRCh38/hg38 1q24.2-25.1(chr1:168314822-175299299)x1 copy number loss See cases [RCV000053918] Chr1:168314822..175299299 [GRCh38]
Chr1:168284060..175268435 [GRCh37]
Chr1:166550684..173535058 [NCBI36]
Chr1:1q24.2-25.1		 pathogenic
NC_000001.11:g.173501975_175305010del deletion Hereditary antithrombin deficiency [RCV001779970] Chr1:173501975..175305010 [GRCh38]
Chr1:1q25.1		 pathogenic
NC_000001.11:g.173850996_173950174del deletion Hereditary antithrombin deficiency [RCV001779996] Chr1:173850996..173950174 [GRCh38]
Chr1:1q25.1		 pathogenic
NC_000001.11:g.172987296_174843232del deletion Hereditary antithrombin deficiency [RCV001779981] Chr1:172987296..174843232 [GRCh38]
Chr1:1q24.3-25.1		 pathogenic
NC_000001.11:g.173859535_173926473del deletion Hereditary antithrombin deficiency [RCV001779973] Chr1:173859535..173926473 [GRCh38]
Chr1:1q25.1		 pathogenic
NC_000001.11:g.173686375_176083118del deletion Hereditary antithrombin deficiency [RCV001779974] Chr1:173686375..176083118 [GRCh38]
Chr1:1q25.1		 pathogenic
NC_000001.11:g.173848142_174816147del deletion Hereditary antithrombin deficiency [RCV001779992] Chr1:173848142..174816147 [GRCh38]
Chr1:1q25.1		 pathogenic
NC_000001.11:g.173787361_174223422del deletion Hereditary antithrombin deficiency [RCV001779997] Chr1:173787361..174223422 [GRCh38]
Chr1:1q25.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:94
Interacting mature miRNAs:95
Transcripts:ENST00000385582
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_003944
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381173,865,622 - 173,865,686 (-)NCBI
GRCh371173,834,771 - 173,834,824 (-)RGD
Build 361172,101,394 - 172,101,447 (-)NCBI Archive
Celera1146,944,240 - 146,944,293 (-)RGD
HuRef1145,059,726 - 145,059,779 (-)ENTREZGENE
CHM1_11175,257,212 - 175,257,265 (-)NCBI
T2T-CHM13v2.01173,223,741 - 173,223,805 (-)NCBI
Sequence:
Promoters
RGD ID:6786909
Promoter ID:HG_KWN:6238
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000363146,   ENST00000385578,   ENST00000385582,   OTTHUMT00000090604
Position:
Human AssemblyChrPosition (strand)Source
Build 361172,101,491 - 172,102,657 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC SNORD78 COSMIC
GTEx SNORD78 GTEx
HGNC ID HGNC:32738 ENTREZGENE
Human Proteome Map SNORD78 Human Proteome Map
NCBI Gene 692198 ENTREZGENE
PharmGKB PA145007773 PharmGKB
RNAcentral URS00006CFC33 RNACentral