SCARNA16 (small Cajal body-specific RNA 16) - Rat Genome Database

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Gene: SCARNA16 (small Cajal body-specific RNA 16) Homo sapiens
Analyze
Symbol: SCARNA16
Name: small Cajal body-specific RNA 16
RGD ID: 1602759
HGNC Page HGNC:32573
Description: Predicted to be involved in RNA processing. Predicted to be located in nucleolus; INTERACTS WITH benzo[a]pyrene; cisplatin; doxorubicin.
Type: ncrna (Ensembl: scaRNA)
RefSeq Status: VALIDATED
Previously known as: ACA47
RGD Orthologs
Mouse
Rat
Dog
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381777,089,307 - 77,089,493 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1777,089,307 - 77,089,493 (+)EnsemblGRCh38hg38GRCh38
GRCh371775,085,389 - 75,085,575 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361772,596,984 - 72,597,170 (+)NCBINCBI36Build 36hg18NCBI36
Celera1771,680,172 - 71,680,358 (+)NCBICelera
Cytogenetic Map17q25.2NCBI
HuRef1770,512,594 - 70,512,780 (+)NCBIHuRef
CHM1_11775,150,303 - 75,150,489 (+)NCBICHM1_1
T2T-CHM13v2.01777,982,158 - 77,982,344 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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)

References
Additional References at PubMed
PMID:15199136   PMID:22658674  


Genomics

Comparative Map Data
SCARNA16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381777,089,307 - 77,089,493 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1777,089,307 - 77,089,493 (+)EnsemblGRCh38hg38GRCh38
GRCh371775,085,389 - 75,085,575 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361772,596,984 - 72,597,170 (+)NCBINCBI36Build 36hg18NCBI36
Celera1771,680,172 - 71,680,358 (+)NCBICelera
Cytogenetic Map17q25.2NCBI
HuRef1770,512,594 - 70,512,780 (+)NCBIHuRef
CHM1_11775,150,303 - 75,150,489 (+)NCBICHM1_1
T2T-CHM13v2.01777,982,158 - 77,982,344 (+)NCBIT2T-CHM13v2.0
Gm25434
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396139,173,063 - 139,173,229 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6139,173,063 - 139,173,229 (-)EnsemblGRCm39 Ensembl
GRCm386139,196,065 - 139,196,231 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6139,196,065 - 139,196,231 (-)EnsemblGRCm38mm10GRCm38
Cytogenetic Map6G1NCBI
Scarna16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85147,908,870 - 147,909,057 (-)NCBIGRCr8
mRatBN7.210102,276,365 - 102,276,548 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10102,276,365 - 102,276,548 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl10106,022,125 - 106,022,308 (+)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map10q32.2NCBI
LOC119869911
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha1110,173,431 - 110,173,612 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01111,254,715 - 111,254,896 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11110,896,360 - 110,896,541 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01110,532,066 - 110,532,247 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01111,401,761 - 111,401,942 (+)NCBIUU_Cfam_GSD_1.0


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q24.3-25.3(chr17:69916435-83102552)x3 copy number gain See cases [RCV000143342] Chr17:69916435..83102552 [GRCh38]
Chr17:67912576..81048189 [GRCh37]
Chr17:65424171..78653717 [NCBI36]
Chr17:17q24.3-25.3		 pathogenic
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3		 pathogenic
GRCh38/hg38 17q24.3-25.3(chr17:69209079-83086677)x3 copy number gain See cases [RCV000052486] Chr17:69209079..83086677 [GRCh38]
Chr17:67205220..81044553 [GRCh37]
Chr17:64716815..78637842 [NCBI36]
Chr17:17q24.3-25.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:83
Interacting mature miRNAs:84
Transcripts:ENST00000515981
Prediction methods:Microtar, 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: ENST00000515981
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1777,089,307 - 77,089,493 (+)Ensembl
RefSeq Acc Id: NR_003013
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381777,089,307 - 77,089,493 (+)NCBI
GRCh371775,085,389 - 75,085,575 (+)RGD
Build 361772,596,984 - 72,597,170 (+)NCBI Archive
Celera1771,680,172 - 71,680,358 (+)RGD
HuRef1770,512,594 - 70,512,780 (+)ENTREZGENE
CHM1_11775,150,303 - 75,150,489 (+)NCBI
T2T-CHM13v2.01777,982,158 - 77,982,344 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SCARNA16 COSMIC
Ensembl Genes ENSG00000275143 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000515981 ENTREZGENE
GTEx ENSG00000275143 GTEx
HGNC ID HGNC:32573 ENTREZGENE
Human Proteome Map SCARNA16 Human Proteome Map
NCBI Gene 677781 ENTREZGENE
PharmGKB PA144596376 PharmGKB
RNAcentral URS000015F227 RNACentral