PSMD6-AS2 (PSMD6 antisense RNA 2) - Rat Genome Database

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Gene: PSMD6-AS2 (PSMD6 antisense RNA 2) Homo sapiens
Analyze
Symbol: PSMD6-AS2
Name: PSMD6 antisense RNA 2
RGD ID: 6766959
HGNC Page HGNC:44125
Description: ASSOCIATED WITH genetic disease; INTERACTS WITH 2-hydroxypropanoic acid; acrylamide; aristolochic acid A
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP11-245J9.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38364,004,022 - 64,012,243 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl364,004,022 - 64,012,148 (+)EnsemblGRCh38hg38GRCh38
GRCh37363,989,698 - 63,997,919 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera364,006,091 - 64,014,691 (+)NCBICelera
Cytogenetic Map3p14.1NCBI
HuRef364,086,765 - 64,094,987 (+)NCBIHuRef
CHM1_1363,941,030 - 63,949,251 (+)NCBICHM1_1
T2T-CHM13v2.0364,047,636 - 64,055,858 (+)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
References
Additional References at PubMed
PMID:14702039   PMID:32393512  


Genomics

Variants

.
Variants in PSMD6-AS2
3 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3p14.1(chr3:63822831-64433817)x1 copy number loss See cases [RCV000139356] Chr3:63822831..64433817 [GRCh38]
Chr3:63808507..64419493 [GRCh37]
Chr3:63783547..64394533 [NCBI36]
Chr3:3p14.1		 uncertain significance
GRCh38/hg38 3p14.3-14.1(chr3:57430538-64884522)x1 copy number loss See cases [RCV000139570] Chr3:57430538..64884522 [GRCh38]
Chr3:57416265..64870197 [GRCh37]
Chr3:57391305..64845237 [NCBI36]
Chr3:3p14.3-14.1		 pathogenic
GRCh38/hg38 3p14.3-11.1(chr3:57140424-90259960)x1 copy number loss See cases [RCV000139626] Chr3:57140424..90259960 [GRCh38]
Chr3:57174452..90309110 [GRCh37]
Chr3:57149492..90391800 [NCBI36]
Chr3:3p14.3-11.1		 pathogenic
GRCh38/hg38 3p21.1-14.1(chr3:54045018-66060461)x1 copy number loss See cases [RCV000051081] Chr3:54045018..66060461 [GRCh38]
Chr3:54079045..66046136 [GRCh37]
Chr3:54054085..66021176 [NCBI36]
Chr3:3p21.1-14.1		 pathogenic
GRCh38/hg38 3p14.2-14.1(chr3:61970847-68465832)x1 copy number loss See cases [RCV000050774] Chr3:61970847..68465832 [GRCh38]
Chr3:61956521..68514983 [GRCh37]
Chr3:61931561..68597673 [NCBI36]
Chr3:3p14.2-14.1		 pathogenic
NM_014814.3(PSMD6):c.1075C>A (p.Pro359Thr) single nucleotide variant Inborn genetic diseases [RCV003305244] Chr3:64010763 [GRCh38]
Chr3:63996439 [GRCh37]
Chr3:3p14.1		 uncertain significance
NM_014814.3(PSMD6):c.1021G>A (p.Gly341Arg) single nucleotide variant Inborn genetic diseases [RCV002993078] Chr3:64010930 [GRCh38]
Chr3:63996606 [GRCh37]
Chr3:3p14.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:33
Count of miRNA genes:29
Interacting mature miRNAs:32
Transcripts:ENST00000472046
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
STS-N50805  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37363,996,249 - 63,996,498UniSTSGRCh37
Build 36363,971,289 - 63,971,538RGDNCBI36
Celera364,013,021 - 64,013,270RGD
Cytogenetic Map3p14UniSTS
Cytogenetic Map3p14.1UniSTS
HuRef364,093,317 - 64,093,566UniSTS
GeneMap99-GB4 RH Map3191.75UniSTS
SHGC-77025  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37363,996,265 - 63,996,442UniSTSGRCh37
Build 36363,971,305 - 63,971,482RGDNCBI36
Celera364,013,037 - 64,013,214RGD
Cytogenetic Map3p14UniSTS
Cytogenetic Map3p14.1UniSTS
HuRef364,093,333 - 64,093,510UniSTS
GeneMap99-GB4 RH Map3191.22UniSTS
NCBI RH Map3512.6UniSTS
G15837  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37363,995,557 - 63,995,656UniSTSGRCh37
Build 36363,970,597 - 63,970,696RGDNCBI36
Celera364,012,329 - 64,012,428RGD
Cytogenetic Map3p14UniSTS
HuRef364,092,625 - 64,092,724UniSTS
SGC30565  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37363,987,551 - 63,987,676UniSTSGRCh37
Build 36363,962,591 - 63,962,716RGDNCBI36
Celera364,004,322 - 64,004,447RGD
Cytogenetic Map3p14UniSTS
Cytogenetic Map3p21.1-p12UniSTS
HuRef364,084,618 - 64,084,743UniSTS
GeneMap99-GB4 RH Map3200.43UniSTS
Whitehead-RH Map3243.0UniSTS


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 14 5 93 19 4 11 17 16 1 1 15
Low 2365 2646 1562 515 1655 358 4286 2046 2160 252 1342 1484 168 1200 2755 4
Below cutoff 60 323 141 96 193 95 49 143 1533 160 83 101 2 3 18

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000472046
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl364,004,022 - 64,012,148 (+)Ensembl
RefSeq Acc Id: NR_038286
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38364,004,022 - 64,012,243 (+)NCBI
GRCh37363,989,698 - 63,997,919 (+)NCBI
HuRef364,086,765 - 64,094,987 (+)NCBI
CHM1_1363,941,030 - 63,949,251 (+)NCBI
T2T-CHM13v2.0364,047,636 - 64,055,858 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC PSMD6-AS2 COSMIC
Ensembl Genes ENSG00000239653 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000472046 ENTREZGENE
GTEx ENSG00000239653 GTEx
HGNC ID HGNC:44125 ENTREZGENE
Human Proteome Map PSMD6-AS2 Human Proteome Map
NCBI Gene PSMD6-AS2 ENTREZGENE
RNAcentral URS000075EC82 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-21 PSMD6-AS2  PSMD6 antisense RNA 2  PSMD6-AS2  PSMD6 antisense RNA 2 (non-protein coding)  Symbol and/or name change 5135510 APPROVED