SNORD87 (small nucleolar RNA, C/D box 87) - Rat Genome Database

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Gene: SNORD87 (small nucleolar RNA, C/D box 87) Homo sapiens
Analyze
Symbol: SNORD87
Name: small nucleolar RNA, C/D box 87
RGD ID: 1602235
HGNC Page HGNC:32746
Description: Predicted to be involved in RNA processing. Predicted to be located in nucleolus.
Type: snorna
RefSeq Status: VALIDATED
Previously known as: HBII-276; U87
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
GRCh38866,922,474 - 66,922,549 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl866,922,467 - 66,922,555 (-)EnsemblGRCh38hg38GRCh38
GRCh37867,834,709 - 67,834,784 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36867,997,263 - 67,997,338 (-)NCBINCBI36Build 36hg18NCBI36
Celera863,828,203 - 63,828,278 (-)NCBICelera
Cytogenetic Map8q13.1NCBI
HuRef863,327,295 - 63,327,370 (-)NCBIHuRef
CHM1_1867,889,730 - 67,889,805 (-)NCBICHM1_1
T2T-CHM13v2.0867,348,953 - 67,349,028 (-)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)

References
Additional References at PubMed
PMID:11387227   PMID:12119114   PMID:16226852   PMID:19446021   PMID:27609421   PMID:32513696  


Genomics

Comparative Map Data
SNORD87
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38866,922,474 - 66,922,549 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl866,922,467 - 66,922,555 (-)EnsemblGRCh38hg38GRCh38
GRCh37867,834,709 - 67,834,784 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36867,997,263 - 67,997,338 (-)NCBINCBI36Build 36hg18NCBI36
Celera863,828,203 - 63,828,278 (-)NCBICelera
Cytogenetic Map8q13.1NCBI
HuRef863,327,295 - 63,327,370 (-)NCBIHuRef
CHM1_1867,889,730 - 67,889,805 (-)NCBICHM1_1
T2T-CHM13v2.0867,348,953 - 67,349,028 (-)NCBIT2T-CHM13v2.0
Snord87
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39110,012,695 - 10,012,768 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl110,012,688 - 10,012,774 (-)EnsemblGRCm39 Ensembl
GRCm3819,942,470 - 9,942,543 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl19,942,463 - 9,942,549 (-)EnsemblGRCm38mm10GRCm38
MGSCv3719,932,551 - 9,932,624 (-)NCBIGRCm37MGSCv37mm9NCBIm37
Celera19,916,497 - 9,916,570 (-)NCBICelera
Cytogenetic Map1A2NCBI
cM Map12.22NCBI
Snord87
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8514,080,356 - 14,080,440 (+)NCBIGRCr8
mRatBN7.259,297,489 - 9,297,573 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl59,297,489 - 9,297,573 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0 Ensembl58,979,349 - 8,979,433 (+)EnsemblRnor6.0rn6Rnor6.0
Cytogenetic Map5q11NCBI
LOC119866814
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha2916,778,243 - 16,778,331 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02916,542,896 - 16,542,984 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12916,575,119 - 16,575,207 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02916,674,978 - 16,675,066 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02916,931,323 - 16,931,411 (-)NCBIUU_Cfam_GSD_1.0


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8q12.1-21.13(chr8:57361243-79170078)x3 copy number gain See cases [RCV000053653] Chr8:57361243..79170078 [GRCh38]
Chr8:58273802..80082313 [GRCh37]
Chr8:58436356..80244868 [NCBI36]
Chr8:8q12.1-21.13		 pathogenic
GRCh38/hg38 8q12.3-21.13(chr8:61691800-82537696)x3 copy number gain See cases [RCV000053654] Chr8:61691800..82537696 [GRCh38]
Chr8:62604359..83449931 [GRCh37]
Chr8:62766913..83612486 [NCBI36]
Chr8:8q12.3-21.13		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:244417-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|See cases [RCV000053604] Chr8:244417..145054775 [GRCh38]
Chr8:194417..146280161 [GRCh37]
Chr8:184417..146250965 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8q12.3-21.11(chr8:62230636-73227786)x1 copy number loss See cases [RCV000054242] Chr8:62230636..73227786 [GRCh38]
Chr8:63143195..74140021 [GRCh37]
Chr8:63305749..74302575 [NCBI36]
Chr8:8q12.3-21.11		 pathogenic
GRCh38/hg38 8q11.1-13.2(chr8:46031334-69303787)x3 copy number gain See cases [RCV000133720] Chr8:46031334..69303787 [GRCh38]
Chr8:46942956..70216022 [GRCh37]
Chr8:47062121..70378576 [NCBI36]
Chr8:8q11.1-13.2		 pathogenic
GRCh38/hg38 8q13.1-22.1(chr8:66171669-93505509)x3 copy number gain See cases [RCV000137050] Chr8:66171669..93505509 [GRCh38]
Chr8:67083904..94517737 [GRCh37]
Chr8:67246458..94586913 [NCBI36]
Chr8:8q13.1-22.1		 pathogenic
GRCh38/hg38 8q13.1-21.13(chr8:66633845-80100089)x3 copy number gain See cases [RCV000138027] Chr8:66633845..80100089 [GRCh38]
Chr8:67546080..81012324 [GRCh37]
Chr8:67708634..81174879 [NCBI36]
Chr8:8q13.1-21.13		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8q11.1-24.3(chr8:46031340-139285494)x3 copy number gain See cases [RCV000139539] Chr8:46031340..139285494 [GRCh38]
Chr8:46942962..140297737 [GRCh37]
Chr8:47062127..140366919 [NCBI36]
Chr8:8q11.1-24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000148092] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh37/hg19 8p12-q24.3(chr8:31936551-146295771)x3 copy number gain not provided [RCV000848192] Chr8:31936551..146295771 [GRCh37]
Chr8:8p12-q24.3		 pathogenic
GRCh37/hg19 8p23.3-q24.3(chr8:158991-146280828)x3 copy number gain See cases [RCV000447507] Chr8:158991..146280828 [GRCh37]
Chr8:8p23.3-q24.3		 pathogenic
GRCh37/hg19 8q12.3-13.2(chr8:65194424-68570319)x1 copy number loss See cases [RCV000445999] Chr8:65194424..68570319 [GRCh37]
Chr8:8q12.3-13.2		 pathogenic
GRCh37/hg19 8p23.3-q24.3(chr8:158049-146295771) copy number gain See cases [RCV000510234] Chr8:158049..146295771 [GRCh37]
Chr8:8p23.3-q24.3		 pathogenic
GRCh37/hg19 8p23.3-q24.3(chr8:158049-146295771)x3 copy number gain See cases [RCV000511095] Chr8:158049..146295771 [GRCh37]
Chr8:8p23.3-q24.3		 pathogenic
GRCh37/hg19 8p23.1-q24.3(chr8:12490999-146295771)x3 copy number gain See cases [RCV000512169] Chr8:12490999..146295771 [GRCh37]
Chr8:8p23.1-q24.3		 pathogenic
GRCh37/hg19 8p23.3-q24.3(chr8:164984-146293414)x3 copy number gain not provided [RCV000747254] Chr8:164984..146293414 [GRCh37]
Chr8:8p23.3-q24.3		 pathogenic
GRCh37/hg19 8p23.3-q24.3(chr8:10213-146293414)x3 copy number gain not provided [RCV000747248] Chr8:10213..146293414 [GRCh37]
Chr8:8p23.3-q24.3		 pathogenic
GRCh37/hg19 8p23.3-q24.3(chr8:158048-146295771)x3 copy number gain not provided [RCV000848478] Chr8:158048..146295771 [GRCh37]
Chr8:8p23.3-q24.3		 pathogenic
GRCh37/hg19 8q13.1-13.2(chr8:67780228-68161496)x3 copy number gain not provided [RCV000848585] Chr8:67780228..68161496 [GRCh37]
Chr8:8q13.1-13.2		 uncertain significance
GRCh37/hg19 8q13.1-13.2(chr8:67828205-68074172)x3 copy number gain not provided [RCV001006110] Chr8:67828205..68074172 [GRCh37]
Chr8:8q13.1-13.2		 likely benign
GRCh37/hg19 8q13.1-13.2(chr8:67718713-68020835)x3 copy number gain not provided [RCV001006109] Chr8:67718713..68020835 [GRCh37]
Chr8:8q13.1-13.2		 uncertain significance
GRCh37/hg19 8q13.1(chr8:67810924-67920345)x1 copy number loss not provided [RCV001258411] Chr8:67810924..67920345 [GRCh37]
Chr8:8q13.1		 uncertain significance
GRCh37/hg19 8q13.1-13.2(chr8:67744375-68387850)x3 copy number gain not provided [RCV001258413] Chr8:67744375..68387850 [GRCh37]
Chr8:8q13.1-13.2		 uncertain significance
NC_000008.10:g.(?_67786376)_(68165857_?)dup duplication Joubert syndrome 21 [RCV001346674] Chr8:67786376..68165857 [GRCh37]
Chr8:8q13.1-13.2		 uncertain significance
GRCh37/hg19 8p23.3-q24.3(chr8:158048-146295771) copy number gain Polydactyly [RCV002280629] Chr8:158048..146295771 [GRCh37]
Chr8:8p23.3-q24.3		 pathogenic
GRCh37/hg19 8q12.3-13.2(chr8:65194424-68570319) copy number loss not specified [RCV002053768] Chr8:65194424..68570319 [GRCh37]
Chr8:8q12.3-13.2		 pathogenic
GRCh37/hg19 8q13.1-13.2(chr8:66045954-69807260)x1 copy number loss not provided [RCV001836560] Chr8:66045954..69807260 [GRCh37]
Chr8:8q13.1-13.2		 pathogenic
GRCh37/hg19 8q13.1-13.2(chr8:67642641-68406704)x1 copy number loss not provided [RCV002473707] Chr8:67642641..68406704 [GRCh37]
Chr8:8q13.1-13.2		 uncertain significance
GRCh37/hg19 8q13.1-13.2(chr8:67261729-68676568)x1 copy number loss not provided [RCV002472760] Chr8:67261729..68676568 [GRCh37]
Chr8:8q13.1-13.2		 uncertain significance
GRCh37/hg19 8p21.2-q21.3(chr8:27024288-89410121)x3 copy number gain not specified [RCV003986754] Chr8:27024288..89410121 [GRCh37]
Chr8:8p21.2-q21.3		 pathogenic
GRCh37/hg19 8p23.3-q24.3(chr8:158048-146295771)x3 copy number gain not specified [RCV003986742] Chr8:158048..146295771 [GRCh37]
Chr8:8p23.3-q24.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:83
Count of miRNA genes:46
Interacting mature miRNAs:46
Transcripts:ENST00000364849, ENST00000522478
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.

Markers in Region
RH47443  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37867,834,267 - 67,834,347UniSTSGRCh37
Build 36867,996,821 - 67,996,901RGDNCBI36
Celera863,827,761 - 63,827,841RGD
Cytogenetic Map8q13UniSTS
Cytogenetic Map8q13.1UniSTS
HuRef863,326,853 - 63,326,933UniSTS
GeneMap99-GB4 RH Map8360.91UniSTS
D8S1363E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37867,834,558 - 67,834,944UniSTSGRCh37
Build 36867,997,112 - 67,997,498RGDNCBI36
Celera863,828,052 - 63,828,438RGD
Cytogenetic Map8q13UniSTS
Cytogenetic Map8q13.1UniSTS
HuRef863,327,144 - 63,327,530UniSTS


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
High
Medium 466 538 704 20 283 4 1518 245 807 18 563 825 16 446 1012
Low 1743 2210 710 362 721 217 2426 1755 2620 91 549 404 145 751 1666
Below cutoff 3 105 6 5 90 5 72 87 80 5 72

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000364849
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl866,922,467 - 66,922,555 (-)Ensembl
RefSeq Acc Id: NR_002598
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38866,922,474 - 66,922,549 (-)NCBI
GRCh37867,834,709 - 67,834,784 (-)RGD
Build 36867,997,263 - 67,997,338 (-)NCBI Archive
Celera863,828,203 - 63,828,278 (-)RGD
HuRef863,327,295 - 63,327,370 (-)RGD
CHM1_1867,889,730 - 67,889,805 (-)NCBI
T2T-CHM13v2.0867,348,953 - 67,349,028 (-)NCBI
Sequence:
Promoters
RGD ID:6807039
Promoter ID:HG_KWN:61431
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000364849
Position:
Human AssemblyChrPosition (strand)Source
Build 36867,996,911 - 67,998,082 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC SNORD87 COSMIC
Ensembl Genes ENSG00000254341 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000364849 ENTREZGENE
GTEx ENSG00000254341 GTEx
HGNC ID HGNC:32746 ENTREZGENE
Human Proteome Map SNORD87 Human Proteome Map
NCBI Gene 641648 ENTREZGENE
OMIM 612216 OMIM
PharmGKB PA145007777 PharmGKB
RNAcentral URS000075BEB6 RNACentral