SOCS2-AS1 (SOCS2 antisense RNA 1) - Rat Genome Database

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Gene: SOCS2-AS1 (SOCS2 antisense RNA 1) Homo sapiens
Analyze
Symbol: SOCS2-AS1
Name: SOCS2 antisense RNA 1
RGD ID: 6768907
HGNC Page HGNC:27054
Description: INTERACTS WITH acrylamide; entinostat; leflunomide
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
GRCh381293,565,628 - 93,571,398 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1293,542,022 - 93,571,768 (-)EnsemblGRCh38hg38GRCh38
GRCh371293,959,404 - 93,965,174 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361292,483,535 - 92,490,109 (-)NCBINCBI36Build 36hg18NCBI36
Celera1293,630,041 - 93,636,615 (-)NCBICelera
Cytogenetic Map12q22NCBI
HuRef1291,026,318 - 91,032,122 (-)NCBIHuRef
CHM1_11293,924,356 - 93,930,126 (-)NCBICHM1_1
T2T-CHM13v2.01293,547,081 - 93,552,851 (-)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:14702039   PMID:24168098   PMID:27342777   PMID:32352013   PMID:32437330   PMID:32688371   PMID:34536509   PMID:37267865   PMID:37677983  


Genomics

Variants

.
Variants in SOCS2-AS1
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12q22(chr12:93374113-94267175)x3 copy number gain See cases [RCV000134720] Chr12:93374113..94267175 [GRCh38]
Chr12:93767889..94660951 [GRCh37]
Chr12:92292020..93185082 [NCBI36]
Chr12:12q22		 uncertain significance
GRCh38/hg38 12q21.33-22(chr12:90996508-94872818)x1 copy number loss See cases [RCV000138659] Chr12:90996508..94872818 [GRCh38]
Chr12:91390285..95266594 [GRCh37]
Chr12:89914416..93790725 [NCBI36]
Chr12:12q21.33-22		 likely pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
GRCh38/hg38 12q21.33-24.11(chr12:91044318-109133210)x3 copy number gain See cases [RCV000142447] Chr12:91044318..109133210 [GRCh38]
Chr12:91438095..109571015 [GRCh37]
Chr12:89962226..108055398 [NCBI36]
Chr12:12q21.33-24.11		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:651
Count of miRNA genes:426
Interacting mature miRNAs:456
Transcripts:ENST00000499137, ENST00000500986, ENST00000547845, ENST00000551626
Prediction methods: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
RH98660  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371293,959,440 - 93,959,569UniSTSGRCh37
Build 361292,483,571 - 92,483,700RGDNCBI36
Celera1293,630,077 - 93,630,206RGD
Cytogenetic Map12q22UniSTS
HuRef1291,026,354 - 91,026,483UniSTS
GeneMap99-GB4 RH Map12363.71UniSTS


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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 146 40 271 6 26 6 14 19 270 2 508 113 1 16 9
Low 2229 2374 1339 490 1297 346 3450 1490 2894 361 856 1433 159 1 1188 2060 5 1
Below cutoff 63 573 115 126 578 112 891 685 568 55 86 67 14 718

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000499137
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1293,542,463 - 93,571,768 (-)Ensembl
RefSeq Acc Id: ENST00000500986
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1293,542,022 - 93,571,768 (-)Ensembl
RefSeq Acc Id: ENST00000547845
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1293,551,433 - 93,567,179 (-)Ensembl
RefSeq Acc Id: ENST00000551626
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1293,565,584 - 93,571,398 (-)Ensembl
RefSeq Acc Id: ENST00000662875
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1293,542,820 - 93,570,854 (-)Ensembl
RefSeq Acc Id: ENST00000668485
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1293,542,463 - 93,570,961 (-)Ensembl
RefSeq Acc Id: NR_038263
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381293,565,628 - 93,571,398 (-)NCBI
GRCh371293,936,237 - 93,965,544 (-)NCBI
HuRef1291,026,318 - 91,032,122 (-)NCBI
CHM1_11293,924,356 - 93,930,126 (-)NCBI
T2T-CHM13v2.01293,547,081 - 93,552,851 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC SOCS2-AS1 COSMIC
Ensembl Genes ENSG00000246985 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000551626 ENTREZGENE
GTEx ENSG00000246985 GTEx
HGNC ID HGNC:27054 ENTREZGENE
Human Proteome Map SOCS2-AS1 Human Proteome Map
NCBI Gene SOCS2-AS1 ENTREZGENE
OMIM 617269 OMIM
RNAcentral URS000075B390 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-21 SOCS2-AS1  SOCS2 antisense RNA 1  SOCS2-AS1  SOCS2 antisense RNA 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED