PHACTR3-AS1 (PHACTR3 antisense RNA 1) - Rat Genome Database

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Gene: PHACTR3-AS1 (PHACTR3 antisense RNA 1) Homo sapiens
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Symbol: PHACTR3-AS1
Name: PHACTR3 antisense RNA 1
RGD ID: 14974414
HGNC Page HGNC:40727
Description:
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
GRCh382059,626,464 - 59,628,289 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2059,624,904 - 59,628,295 (-)EnsemblGRCh38hg38GRCh38
GRCh372058,201,519 - 58,203,344 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map20q13.32NCBI
HuRef2054,988,982 - 54,990,807 (-)NCBIHuRef
CHM1_12058,102,612 - 58,104,437 (-)NCBICHM1_1
T2T-CHM13v2.02061,410,696 - 61,412,521 (-)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 20q13.2-13.33(chr20:56198032-64277321)x3 copy number gain See cases [RCV000138035] Chr20:56198032..64277321 [GRCh38]
Chr20:54773088..62908674 [GRCh37]
Chr20:54206495..62379118 [NCBI36]
Chr20:20q13.2-13.33		 pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:53236165-64284202)x3 copy number gain See cases [RCV000143584] Chr20:53236165..64284202 [GRCh38]
Chr20:51852704..62915555 [GRCh37]
Chr20:51286111..62385999 [NCBI36]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh38/hg38 20q13.12-13.33(chr20:44787704-64277321)x3 copy number gain See cases [RCV000053035] Chr20:44787704..64277321 [GRCh38]
Chr20:43416345..62908674 [GRCh37]
Chr20:42849759..62379118 [NCBI36]
Chr20:20q13.12-13.33		 pathogenic
GRCh38/hg38 20q13.32-13.33(chr20:59041966-64277321)x3 copy number gain See cases [RCV000135805] Chr20:59041966..64277321 [GRCh38]
Chr20:57617021..62908674 [GRCh37]
Chr20:57050416..62379118 [NCBI36]
Chr20:20q13.32-13.33		 pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:55630597-60941207)x3 copy number gain See cases [RCV000135622] Chr20:55630597..60941207 [GRCh38]
Chr20:54220678..59516263 [GRCh37]
Chr20:53639062..58949658 [NCBI36]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh38/hg38 20q13.31-13.33(chr20:57229415-64273089)x3 copy number gain See cases [RCV000141347] Chr20:57229415..64273089 [GRCh38]
Chr20:55804471..62904442 [GRCh37]
Chr20:55237878..62374886 [NCBI36]
Chr20:20q13.31-13.33		 pathogenic
GRCh38/hg38 20q13.13-13.33(chr20:50805746-64334135) copy number gain 20q13.13qter duplication [RCV004555205] Chr20:50805746..64334135 [GRCh38]
Chr20:20q13.13-13.33		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:592
Count of miRNA genes:312
Interacting mature miRNAs:320
Transcripts:ENST00000443055, ENST00000451510
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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2292864PRSTS43_HProstate tumor susceptibility QTL 43 (human)0.620.05Prostate tumor susceptibility204730303964444167Human
1300007BP29_HBlood pressure QTL 29 (human)Blood pressurehypertension susceptibility203653600562536005Human


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
sensory system
59 253 420 109 2990 145 189 33 120 18 199 444 368 3085 72 273 159 16

Sequence


Ensembl Acc Id: ENST00000443055
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2059,626,464 - 59,628,279 (-)Ensembl
Ensembl Acc Id: ENST00000451510
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2059,626,481 - 59,628,289 (-)Ensembl
Ensembl Acc Id: ENST00000663583
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2059,624,909 - 59,628,268 (-)Ensembl
Ensembl Acc Id: ENST00000668717
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2059,624,904 - 59,628,295 (-)Ensembl
RefSeq Acc Id: NR_040513
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382059,626,464 - 59,628,289 (-)NCBI
T2T-CHM13v2.02061,410,696 - 61,412,521 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC PHACTR3-AS1 COSMIC
Ensembl Genes ENSG00000238194 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000443055 ENTREZGENE
GTEx ENSG00000238194 GTEx
HGNC ID HGNC:40727 ENTREZGENE
Human Proteome Map PHACTR3-AS1 Human Proteome Map
NCBI Gene PHACTR3-AS1 ENTREZGENE
RNAcentral URS00004F7152 RNACentral
  URS00005A389F RNACentral
  URS000075DD70 RNACentral
  URS0000EF108E RNACentral
  URS0000EF59C2 RNACentral