SHANK2-AS3 (SHANK2 antisense RNA 3) - Rat Genome Database

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Gene: SHANK2-AS3 (SHANK2 antisense RNA 3) Homo sapiens
Analyze
Symbol: SHANK2-AS3
Name: SHANK2 antisense RNA 3
RGD ID: 7204625
HGNC Page HGNC:25098
Description: INTERACTS WITH 2-palmitoylglycerol; clothianidin
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C11orf76
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381170,862,790 - 70,865,115 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1170,862,790 - 70,865,115 (+)EnsemblGRCh38hg38GRCh38
GRCh371170,708,895 - 70,711,220 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361170,387,089 - 70,387,662 (+)NCBINCBI36Build 36hg18NCBI36
Celera1167,970,780 - 67,973,105 (+)NCBICelera
Cytogenetic Map11q13.4NCBI
HuRef1166,970,727 - 66,973,052 (+)NCBIHuRef
CHM1_11170,592,314 - 70,594,639 (+)NCBICHM1_1
T2T-CHM13v2.01170,884,034 - 70,886,359 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 11q13.4(chr11:70575193-70893208)x1 copy number loss See cases [RCV000141941] Chr11:70575193..70893208 [GRCh38]
Chr11:70421298..70739313 [GRCh37]
Chr11:70098946..70416961 [NCBI36]
Chr11:11q13.4		 uncertain significance
GRCh38/hg38 11q13.2-13.4(chr11:68031693-71593495)x1 copy number loss See cases [RCV000142138] Chr11:68031693..71593495 [GRCh38]
Chr11:67799160..71304541 [GRCh37]
Chr11:67555736..70982189 [NCBI36]
Chr11:11q13.2-13.4		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:199
Count of miRNA genes:192
Interacting mature miRNAs:198
Transcripts:ENST00000307548
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 4
Low 12 1 9 3 56 3 19 16 25 9 17 52 1 1
Below cutoff 360 146 425 172 210 113 575 127 369 163 311 528 70 67 232 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000307548
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1170,862,790 - 70,865,115 (+)Ensembl
RefSeq Acc Id: NR_073536
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381170,862,790 - 70,865,115 (+)NCBI
HuRef1166,970,727 - 66,973,052 (+)NCBI
CHM1_11170,592,314 - 70,594,639 (+)NCBI
T2T-CHM13v2.01170,884,034 - 70,886,359 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein AAH04224 (Get FASTA)   NCBI Sequence Viewer  
  EAW74783 (Get FASTA)   NCBI Sequence Viewer  
  Q9BTD1 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9BTD1-F1-model_v2 AlphaFold Q9BTD1 1-123 view protein structure


Additional Information

Database Acc Id Source(s)
COSMIC SHANK2-AS3 COSMIC
Ensembl Genes ENSG00000171671 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000307548 ENTREZGENE
GTEx ENSG00000171671 GTEx
HGNC ID HGNC:25098 ENTREZGENE
Human Proteome Map SHANK2-AS3 Human Proteome Map
NCBI Gene SHANK2-AS3 ENTREZGENE
PharmGKB PA144596495 PharmGKB
RNAcentral URS000075D7DD RNACentral
UniProt Q9BTD1 ENTREZGENE, UniProtKB/Swiss-Prot