PRICKLE2-DT (PRICKLE2 divergent transcript) - Rat Genome Database

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Gene: PRICKLE2-DT (PRICKLE2 divergent transcript) Homo sapiens
Analyze
Symbol: PRICKLE2-DT
Name: PRICKLE2 divergent transcript
RGD ID: 14402232
HGNC Page HGNC:52829
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
GRCh38364,445,257 - 64,456,070 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl364,445,231 - 64,456,070 (+)EnsemblGRCh38hg38GRCh38
GRCh37364,430,933 - 64,441,746 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3p14.1NCBI
HuRef364,528,056 - 64,533,373 (+)NCBIHuRef
CHM1_1364,382,729 - 64,388,047 (+)NCBICHM1_1
T2T-CHM13v2.0364,488,843 - 64,499,659 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics

Variants

.
Variants in PRICKLE2-DT
3 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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
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 3p14.3-14.1(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
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:205
Count of miRNA genes:196
Interacting mature miRNAs:204
Transcripts:ENST00000487097
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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
407101058GWAS750034_Hvital capacity QTL GWAS750034 (human)6e-11vital capacity36444605464446055Human
407190662GWAS839638_Hpeak expiratory flow QTL GWAS839638 (human)2e-11peak expiratory flowmaximum mid-expiratory flow (MMEF) (CMO:0000253)36444880564448806Human
407290787GWAS939763_Hcortical thickness QTL GWAS939763 (human)3e-15cortical thickness36444880564448806Human
406930539GWAS579515_Hsmoking cessation QTL GWAS579515 (human)5e-09smoking cessation36444605464446055Human
407031320GWAS680296_Hpeak expiratory flow QTL GWAS680296 (human)1e-12peak expiratory flowmaximum mid-expiratory flow (MMEF) (CMO:0000253)36444880564448806Human
406996494GWAS645470_Hsmoking cessation QTL GWAS645470 (human)1e-09smoking cessation36444605464446055Human
1331643COPD16_HChronic obstructive pulmonary disease QTL 16 (human)1.07Chronic airflow obstructionpost-BD FEV1 minus pre-BD FEV1/pre-BD FEV1 x 10034938065175380651Human


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
24 130 44 52 244 109 245 84 128 55 113 399 243 3 150 111 581 174 32

Sequence


Ensembl Acc Id: ENST00000487097
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl364,445,231 - 64,454,832 (+)Ensembl
Ensembl Acc Id: ENST00000659263
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl364,445,287 - 64,456,070 (+)Ensembl
Ensembl Acc Id: ENST00000762005
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl364,445,340 - 64,452,476 (+)Ensembl
Ensembl Acc Id: ENST00000762006
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl364,445,248 - 64,448,819 (+)Ensembl
RefSeq Acc Id: NR_183712
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38364,445,257 - 64,456,070 (+)NCBI
T2T-CHM13v2.0364,488,843 - 64,499,659 (+)NCBI
RefSeq Acc Id: NR_183714
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38364,445,257 - 64,456,070 (+)NCBI
T2T-CHM13v2.0364,488,843 - 64,499,659 (+)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC PRICKLE2-DT COSMIC
Ensembl Genes ENSG00000244564 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000659263 ENTREZGENE
GTEx ENSG00000244564 GTEx
HGNC ID HGNC:52829 ENTREZGENE
Human Proteome Map PRICKLE2-DT Human Proteome Map
NCBI Gene PRICKLE2-DT ENTREZGENE
RNAcentral URS00026A2504 RNACentral
  URS00026A283B RNACentral