SNHG27 (small nucleolar RNA host gene 27) - Rat Genome Database

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Gene: SNHG27 (small nucleolar RNA host gene 27) Homo sapiens
Analyze
Symbol: SNHG27
Name: small nucleolar RNA host gene 27
RGD ID: 12903117
HGNC Page HGNC:53481
Description: INTERACTS WITH O-methyleugenol
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384131,764,838 - 131,791,482 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4131,727,587 - 131,791,492 (+)EnsemblGRCh38hg38GRCh38
GRCh374132,685,993 - 132,712,637 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map4q28.3NCBI
HuRef4128,415,069 - 128,441,561 (+)NCBIHuRef
CHM1_14132,662,635 - 132,689,123 (+)NCBICHM1_1
T2T-CHM13v2.04135,088,629 - 135,115,270 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q28.2-31.21(chr4:128119872-142431375)x1 copy number loss See cases [RCV000051056] Chr4:128119872..142431375 [GRCh38]
Chr4:129041027..143352528 [GRCh37]
Chr4:129260477..143571978 [NCBI36]
Chr4:4q28.2-31.21		 pathogenic
GRCh38/hg38 4q22.2-32.3(chr4:92913386-165299707)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|See cases [RCV000051775] Chr4:92913386..165299707 [GRCh38]
Chr4:93834537..166220859 [GRCh37]
Chr4:94053560..166440309 [NCBI36]
Chr4:4q22.2-32.3		 pathogenic
GRCh38/hg38 4q22.3-28.3(chr4:96092893-136410207)x3 copy number gain See cases [RCV000051776] Chr4:96092893..136410207 [GRCh38]
Chr4:97014044..137331362 [GRCh37]
Chr4:97233067..137550812 [NCBI36]
Chr4:4q22.3-28.3		 pathogenic
GRCh38/hg38 4q26-35.2(chr4:118065569-190042639)x3 copy number gain See cases [RCV000051785] Chr4:118065569..190042639 [GRCh38]
Chr4:118986724..190828225 [GRCh37]
Chr4:119206172..191200788 [NCBI36]
Chr4:4q26-35.2		 pathogenic
GRCh38/hg38 4q27-35.2(chr4:121518223-190062270)x3 copy number gain See cases [RCV000051786] Chr4:121518223..190062270 [GRCh38]
Chr4:122439378..190828225 [GRCh37]
Chr4:122658828..191220419 [NCBI36]
Chr4:4q27-35.2		 pathogenic
GRCh38/hg38 4q26-31.21(chr4:116630862-145429900)x1 copy number loss See cases [RCV000053321] Chr4:116630862..145429900 [GRCh38]
Chr4:117552018..146351052 [GRCh37]
Chr4:117771466..146570502 [NCBI36]
Chr4:4q26-31.21		 pathogenic
GRCh38/hg38 4q28.1-28.3(chr4:125118620-132773079)x1 copy number loss See cases [RCV000135316] Chr4:125118620..132773079 [GRCh38]
Chr4:126039775..133694234 [GRCh37]
Chr4:126259225..133913684 [NCBI36]
Chr4:4q28.1-28.3		 pathogenic
GRCh38/hg38 4q26-28.3(chr4:117351881-133565667)x1 copy number loss See cases [RCV000143207] Chr4:117351881..133565667 [GRCh38]
Chr4:118273037..134486822 [GRCh37]
Chr4:118492485..134706272 [NCBI36]
Chr4:4q26-28.3		 pathogenic
GRCh38/hg38 4q28.3(chr4:131345585-131985312)x3 copy number gain See cases [RCV000135802] Chr4:131345585..131985312 [GRCh38]
Chr4:132266740..132906467 [GRCh37]
Chr4:132486190..133125917 [NCBI36]
Chr4:4q28.3		 uncertain significance
GRCh38/hg38 4q28.1-35.1(chr4:125432943-185761887)x3 copy number gain See cases [RCV000138578] Chr4:125432943..185761887 [GRCh38]
Chr4:126354098..186683041 [GRCh37]
Chr4:126573548..186920035 [NCBI36]
Chr4:4q28.1-35.1		 pathogenic|likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:186
Count of miRNA genes:173
Interacting mature miRNAs:176
Transcripts:ENST00000507332, ENST00000507933, ENST00000514222
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 3 1 3 339 1
Low 17 7 90 20 106 20 62 20 28 16 115 96 2 40 2
Below cutoff 900 676 634 126 368 84 1205 652 1066 155 407 616 44 372 776 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000507332
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,773,565 - 131,791,482 (+)Ensembl
RefSeq Acc Id: ENST00000507933
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,773,302 - 131,774,692 (+)Ensembl
RefSeq Acc Id: ENST00000514222
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,750,059 - 131,774,899 (+)Ensembl
RefSeq Acc Id: ENST00000653283
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,747,561 - 131,774,899 (+)Ensembl
RefSeq Acc Id: ENST00000654278
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,764,819 - 131,791,492 (+)Ensembl
RefSeq Acc Id: ENST00000655257
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,732,623 - 131,774,899 (+)Ensembl
RefSeq Acc Id: ENST00000657219
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,772,557 - 131,774,903 (+)Ensembl
RefSeq Acc Id: ENST00000657220
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,727,587 - 131,791,487 (+)Ensembl
RefSeq Acc Id: ENST00000657961
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,764,831 - 131,774,897 (+)Ensembl
RefSeq Acc Id: ENST00000658913
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,750,082 - 131,774,718 (+)Ensembl
RefSeq Acc Id: ENST00000662181
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,764,829 - 131,774,899 (+)Ensembl
RefSeq Acc Id: ENST00000663369
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,757,479 - 131,774,899 (+)Ensembl
RefSeq Acc Id: ENST00000663882
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,757,492 - 131,774,718 (+)Ensembl
RefSeq Acc Id: ENST00000664137
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,772,537 - 131,775,036 (+)Ensembl
RefSeq Acc Id: ENST00000664412
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,749,991 - 131,774,899 (+)Ensembl
RefSeq Acc Id: ENST00000667068
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4131,745,092 - 131,774,899 (+)Ensembl
RefSeq Acc Id: NR_125883
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384131,764,838 - 131,774,899 (+)NCBI
CHM1_14132,662,479 - 132,672,539 (+)NCBI
T2T-CHM13v2.04135,088,629 - 135,098,688 (+)NCBI
Sequence:
RefSeq Acc Id: NR_125884
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384131,764,838 - 131,791,482 (+)NCBI
CHM1_14132,662,479 - 132,689,123 (+)NCBI
T2T-CHM13v2.04135,088,629 - 135,115,270 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SNHG27 COSMIC
Ensembl Genes ENSG00000251676 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000654278 ENTREZGENE
  ENST00000662181 ENTREZGENE
GTEx ENSG00000251676 GTEx
HGNC ID HGNC:53481 ENTREZGENE
Human Proteome Map SNHG27 Human Proteome Map
NCBI Gene SNHG27 ENTREZGENE
RNAcentral URS00007E472B RNACentral
  URS00007E4A15 RNACentral