SNORD113-3 (small nucleolar RNA, C/D box 113-3) - Rat Genome Database

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Gene: SNORD113-3 (small nucleolar RNA, C/D box 113-3) Homo sapiens
Analyze
Symbol: SNORD113-3
Name: small nucleolar RNA, C/D box 113-3
RGD ID: 1602530
HGNC Page HGNC:32982
Description: Predicted to be involved in RNA processing. Predicted to be located in nucleolus.
Type: snorna
RefSeq Status: VALIDATED
Previously known as: 14q(I-3)
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
GRCh3814100,929,919 - 100,929,989 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl14100,929,919 - 100,929,990 (+)EnsemblGRCh38hg38GRCh38
GRCh3714101,396,256 - 101,396,326 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3614100,466,009 - 100,466,079 (+)NCBINCBI36Build 36hg18NCBI36
Celera1481,450,087 - 81,450,157 (+)NCBICelera
Cytogenetic Map14q32.31NCBI
HuRef1481,577,888 - 81,577,958 (+)NCBIHuRef
CHM1_114101,334,451 - 101,334,521 (+)NCBICHM1_1
T2T-CHM13v2.01495,165,348 - 95,165,418 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleolus  (IEA)

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:12045206   PMID:19446021  


Genomics

Comparative Map Data
SNORD113-3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3814100,929,919 - 100,929,989 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl14100,929,919 - 100,929,990 (+)EnsemblGRCh38hg38GRCh38
GRCh3714101,396,256 - 101,396,326 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3614100,466,009 - 100,466,079 (+)NCBINCBI36Build 36hg18NCBI36
Celera1481,450,087 - 81,450,157 (+)NCBICelera
Cytogenetic Map14q32.31NCBI
HuRef1481,577,888 - 81,577,958 (+)NCBIHuRef
CHM1_114101,334,451 - 101,334,521 (+)NCBICHM1_1
T2T-CHM13v2.01495,165,348 - 95,165,418 (+)NCBIT2T-CHM13v2.0
Gm24564
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3912109,597,508 - 109,597,582 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl12109,597,508 - 109,597,582 (+)EnsemblGRCm39 Ensembl
GRCm3812109,631,074 - 109,631,148 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl12109,631,074 - 109,631,148 (+)EnsemblGRCm38mm10GRCm38
Cytogenetic Map12F1NCBI
Snord113-3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86134,367,792 - 134,367,862 (+)NCBIGRCr8
mRatBN7.26128,585,558 - 128,585,628 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl6128,585,558 - 128,585,628 (+)NCBImRatBN7.2 Ensembl
mRatBN7.2 Ensembl6128,585,558 - 128,585,628 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl6133,753,217 - 133,753,287 (+)NCBIRnor6.0rn6Rnor6.0
Cytogenetic Map6q32NCBI
LOC119873111
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha868,672,459 - 68,672,530 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0869,438,215 - 69,438,286 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1869,099,916 - 69,099,987 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0869,165,777 - 69,165,848 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0869,563,962 - 69,564,033 (+)NCBIUU_Cfam_GSD_1.0


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 14q32.2-32.33(chr14:99831655-106855263)x1 copy number loss See cases [RCV000133831] Chr14:99831655..106855263 [GRCh38]
Chr14:100297992..107263478 [GRCh37]
Chr14:99367745..106334523 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q24.3-32.33(chr14:73655772-106879298)x3 copy number gain See cases [RCV000134000] Chr14:73655772..106879298 [GRCh38]
Chr14:74122475..107287505 [GRCh37]
Chr14:73192228..106358550 [NCBI36]
Chr14:14q24.3-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:97638520-106855263)x3 copy number gain See cases [RCV000135400] Chr14:97638520..106855263 [GRCh38]
Chr14:98104857..107263478 [GRCh37]
Chr14:97174610..106334523 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100309382-105987610)x3 copy number gain See cases [RCV000135410] Chr14:100309382..105987610 [GRCh38]
Chr14:100775719..106453697 [GRCh37]
Chr14:99845472..105524742 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:99448012-106850609)x3 copy number gain See cases [RCV000135875] Chr14:99448012..106850609 [GRCh38]
Chr14:99914349..107258824 [GRCh37]
Chr14:98984102..106329869 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20151149-106855263)x3 copy number gain See cases [RCV000135543] Chr14:20151149..106855263 [GRCh38]
Chr14:20619308..107263478 [GRCh37]
Chr14:19689148..106334523 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
GRCh38/hg38 14q32.12-32.33(chr14:92540983-104863658)x3 copy number gain See cases [RCV000135896] Chr14:92540983..104863658 [GRCh38]
Chr14:93007328..105329995 [GRCh37]
Chr14:92077081..104401040 [NCBI36]
Chr14:14q32.12-32.33		 pathogenic
GRCh38/hg38 14q32.13-32.33(chr14:95524407-106879501)x1 copy number loss See cases [RCV000136032] Chr14:95524407..106879501 [GRCh38]
Chr14:95990744..107287708 [GRCh37]
Chr14:95060497..106358753 [NCBI36]
Chr14:14q32.13-32.33		 pathogenic
GRCh38/hg38 14q24.3-32.33(chr14:77222795-106879298)x3 copy number gain See cases [RCV000138230] Chr14:77222795..106879298 [GRCh38]
Chr14:77689138..107287505 [GRCh37]
Chr14:76758891..106358550 [NCBI36]
Chr14:14q24.3-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.31(chr14:100262836-102500697)x1 copy number loss See cases [RCV000139723] Chr14:100262836..102500697 [GRCh38]
Chr14:100729173..102967034 [GRCh37]
Chr14:99798926..102036787 [NCBI36]
Chr14:14q32.2-32.31		 pathogenic
GRCh38/hg38 14q32.2-32.31(chr14:99794337-100944567)x1 copy number loss See cases [RCV000141596] Chr14:99794337..100944567 [GRCh38]
Chr14:100260674..101410904 [GRCh37]
Chr14:99330427..100480657 [NCBI36]
Chr14:14q32.2-32.31		 pathogenic
GRCh38/hg38 14q32.2-32.31(chr14:99930669-101022599)x1 copy number loss See cases [RCV000142774] Chr14:99930669..101022599 [GRCh38]
Chr14:100397006..101488936 [GRCh37]
Chr14:99466759..100558689 [NCBI36]
Chr14:14q32.2-32.31		 pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20043514-106877229)x3 copy number gain See cases [RCV000143373] Chr14:20043514..106877229 [GRCh38]
Chr14:20511673..107285437 [GRCh37]
Chr14:19581513..106356482 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100582059-106877229)x1 copy number loss See cases [RCV000143662] Chr14:100582059..106877229 [GRCh38]
Chr14:101048396..107285437 [GRCh37]
Chr14:100118149..106356482 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
NC_000014.9:g.100806482_101281031del474550 deletion Paternal uniparental disomy of chromosome 14 [RCV000149429] Chr14:100806482..101281031 [GRCh38]
Chr14:101272819..101747368 [GRCh37]
Chr14:14q32.2-32.31		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100590353-106855264)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051553]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051553]|See cases [RCV000051553] Chr14:100590353..106855264 [GRCh38]
Chr14:101056690..107263479 [GRCh37]
Chr14:100126443..106334524 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100309382-106855263)x1 copy number loss See cases [RCV000050938] Chr14:100309382..106855263 [GRCh38]
Chr14:100775719..107263478 [GRCh37]
Chr14:99845472..106334523 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q31.2-32.33(chr14:83912345-106855405)x3 copy number gain See cases [RCV000052294] Chr14:83912345..106855405 [GRCh38]
Chr14:84378689..107263620 [GRCh37]
Chr14:83448442..106334665 [NCBI36]
Chr14:14q31.2-32.33		 pathogenic
GRCh38/hg38 14q31.3-32.33(chr14:86094030-106832642)x3 copy number gain See cases [RCV000052295] Chr14:86094030..106832642 [GRCh38]
Chr14:86560374..107240869 [GRCh37]
Chr14:85630127..106311914 [NCBI36]
Chr14:14q31.3-32.33		 pathogenic
GRCh38/hg38 14q32.12-32.33(chr14:91455861-106832642)x3 copy number gain See cases [RCV000052296] Chr14:91455861..106832642 [GRCh38]
Chr14:91922205..107240869 [GRCh37]
Chr14:90991958..106311914 [NCBI36]
Chr14:14q32.12-32.33		 pathogenic
GRCh38/hg38 14q32.13-32.33(chr14:94628219-106451054)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052298]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052298]|See cases [RCV000052298] Chr14:94628219..106451054 [GRCh38]
Chr14:95094556..106906960 [GRCh37]
Chr14:94164309..105978005 [NCBI36]
Chr14:14q32.13-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:100808300-106855263)x1 copy number loss See cases [RCV000051113] Chr14:100808300..106855263 [GRCh38]
Chr14:101274637..107263478 [GRCh37]
Chr14:100344390..106334523 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
GRCh38/hg38 14q32.2-32.33(chr14:97938637-106855263)x1 copy number loss See cases [RCV000050696] Chr14:97938637..106855263 [GRCh38]
Chr14:98404974..107263478 [GRCh37]
Chr14:97474727..106334523 [NCBI36]
Chr14:14q32.2-32.33		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:59
Count of miRNA genes:58
Interacting mature miRNAs:58
Transcripts:ENST00000364830
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 3 1 20 14 11 14 13 13 48 4 31 23 1 1 1
Low 15 16 70 53 29 54 44 26 107 45 79 48 4 2 4 1
Below cutoff 5 1 6 5 3 2 56 5 7 7 3 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000364830
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl14100,929,919 - 100,929,990 (+)Ensembl
RefSeq Acc Id: NR_003231
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3814100,929,919 - 100,929,989 (+)NCBI
GRCh3714101,396,256 - 101,396,326 (+)RGD
Build 3614100,466,009 - 100,466,079 (+)NCBI Archive
Celera1481,450,087 - 81,450,157 (+)RGD
HuRef1481,577,888 - 81,577,958 (+)ENTREZGENE
CHM1_114101,334,451 - 101,334,521 (+)NCBI
T2T-CHM13v2.01495,165,348 - 95,165,418 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SNORD113-3 COSMIC
Ensembl Genes ENSG00000201700 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000364830 ENTREZGENE
GTEx ENSG00000201700 GTEx
HGNC ID HGNC:32982 ENTREZGENE
Human Proteome Map SNORD113-3 Human Proteome Map
NCBI Gene 767563 ENTREZGENE
PharmGKB PA162404173 PharmGKB
RNAcentral URS000075A0ED RNACentral