SLC9A9-AS1 (SLC9A9 antisense RNA 1) - Rat Genome Database

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Gene: SLC9A9-AS1 (SLC9A9 antisense RNA 1) Homo sapiens
Analyze
Symbol: SLC9A9-AS1
Name: SLC9A9 antisense RNA 1
RGD ID: 6483989
HGNC Page HGNC:40928
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP13-635I23.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383143,342,246 - 143,347,071 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3143,342,246 - 143,347,071 (+)EnsemblGRCh38hg38GRCh38
GRCh373143,061,088 - 143,065,913 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3q24ENTREZGENE
HuRef3140,433,297 - 140,438,118 (+)NCBIHuRef
CHM1_13143,024,024 - 143,028,850 (+)NCBICHM1_1
T2T-CHM13v2.03146,089,586 - 146,094,411 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:16344560  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q22.3-24(chr3:137932000-144468739)x1 copy number loss See cases [RCV000134711] Chr3:137932000..144468739 [GRCh38]
Chr3:137650842..144187581 [GRCh37]
Chr3:139133532..145670271 [NCBI36]
Chr3:3q22.3-24		 pathogenic
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q23-24(chr3:142780798-146233927)x1 copy number loss See cases [RCV000135827] Chr3:142780798..146233927 [GRCh38]
Chr3:142499640..145951714 [GRCh37]
Chr3:143982330..147434404 [NCBI36]
Chr3:3q23-24		 uncertain significance
GRCh38/hg38 3q22.1-24(chr3:129817243-143381624)x1 copy number loss See cases [RCV000136558] Chr3:129817243..143381624 [GRCh38]
Chr3:129536086..143100466 [GRCh37]
Chr3:131018776..144583156 [NCBI36]
Chr3:3q22.1-24		 pathogenic
GRCh38/hg38 3q22.2-25.1(chr3:134257180-149729538)x1 copy number loss See cases [RCV000138135] Chr3:134257180..149729538 [GRCh38]
Chr3:133976022..149447325 [GRCh37]
Chr3:135458712..150930015 [NCBI36]
Chr3:3q22.2-25.1		 pathogenic|likely benign
GRCh38/hg38 3q22.3-24(chr3:137991123-143618786)x1 copy number loss See cases [RCV000139135] Chr3:137991123..143618786 [GRCh38]
Chr3:137709965..143337628 [GRCh37]
Chr3:139192655..144820318 [NCBI36]
Chr3:3q22.3-24		 pathogenic
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24		 pathogenic
GRCh38/hg38 3q22.1-24(chr3:132716978-144784743)x1 copy number loss See cases [RCV000143634] Chr3:132716978..144784743 [GRCh38]
Chr3:132435822..144503585 [GRCh37]
Chr3:133918512..145986275 [NCBI36]
Chr3:3q22.1-24		 pathogenic
GRCh38/hg38 3q22.3-29(chr3:137126982-198110178)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|See cases [RCV000051723] Chr3:137126982..198110178 [GRCh38]
Chr3:136845824..197837049 [GRCh37]
Chr3:138328514..199321446 [NCBI36]
Chr3:3q22.3-29		 pathogenic
GRCh38/hg38 3q22.2-24(chr3:135227451-145870770)x1 copy number loss See cases [RCV000051572] Chr3:135227451..145870770 [GRCh38]
Chr3:134946293..145588557 [GRCh37]
Chr3:136428983..147071247 [NCBI36]
Chr3:3q22.2-24		 pathogenic
GRCh38/hg38 3q23-24(chr3:141751960-148246189)x1 copy number loss See cases [RCV000051575] Chr3:141751960..148246189 [GRCh38]
Chr3:141470802..147963976 [GRCh37]
Chr3:142953492..149446666 [NCBI36]
Chr3:3q23-24		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:72
Interacting mature miRNAs:73
Transcripts:ENST00000479030
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


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 2 2
Low 1 5 30 75 16 2 3 2 157 37 4 7
Below cutoff 386 354 392 59 286 29 807 217 467 58 371 406 30 259 457

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000479030
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3143,342,246 - 143,347,071 (+)Ensembl
RefSeq Acc Id: NR_048544
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383143,342,246 - 143,347,071 (+)NCBI
GRCh373143,061,088 - 143,065,913 (+)NCBI
HuRef3140,433,297 - 140,438,118 (+)NCBI
CHM1_13143,024,024 - 143,028,850 (+)NCBI
T2T-CHM13v2.03146,089,586 - 146,094,411 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SLC9A9-AS1 COSMIC
Ensembl Genes ENSG00000240012 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000479030 ENTREZGENE
GTEx ENSG00000240012 GTEx
HGNC ID HGNC:40928 ENTREZGENE
Human Proteome Map SLC9A9-AS1 Human Proteome Map
NCBI Gene SLC9A9-AS1 ENTREZGENE
RNAcentral URS0000526B62 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-21 SLC9A9-AS1  SLC9A9 antisense RNA 1  SLC9A9-AS1  SLC9A9 antisense RNA 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED