DPY19L3-DT (DPY19L3 divergent transcript) - Rat Genome Database

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Gene: DPY19L3-DT (DPY19L3 divergent transcript) Homo sapiens
Analyze
Symbol: DPY19L3-DT
Name: DPY19L3 divergent transcript
RGD ID: 16564509
HGNC Page HGNC:55307
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC007773.1; LOC400684; novel transcript, antisense to DPY19L3; uncharacterized LOC400684
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381932,390,050 - 32,405,539 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1932,390,050 - 32,405,560 (-)EnsemblGRCh38hg38GRCh38
GRCh371932,880,956 - 32,896,445 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map19q13.11NCBI
HuRef1929,383,999 - 29,399,497 (-)NCBIHuRef
CHM1_11932,882,015 - 32,897,510 (-)NCBICHM1_1
T2T-CHM13v2.01934,908,692 - 34,924,194 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932   PMID:19416867  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19q12-13.13(chr19:29671324-37902990)x1 copy number loss See cases [RCV000136794] Chr19:29671324..37902990 [GRCh38]
Chr19:30162231..38393630 [GRCh37]
Chr19:34854071..43085470 [NCBI36]
Chr19:19q12-13.13		 pathogenic
GRCh38/hg38 19q12-13.13(chr19:29661858-38114723)x1 copy number loss See cases [RCV000135879] Chr19:29661858..38114723 [GRCh38]
Chr19:30152765..38605363 [GRCh37]
Chr19:34844605..43297203 [NCBI36]
Chr19:19q12-13.13		 pathogenic
GRCh38/hg38 19p13.11-q13.11(chr19:17176767-34924150)x3 copy number gain See cases [RCV000050635] Chr19:17176767..34924150 [GRCh38]
Chr19:17287576..35415054 [GRCh37]
Chr19:17148576..40106894 [NCBI36]
Chr19:19p13.11-q13.11		 pathogenic
GRCh38/hg38 19q12-13.12(chr19:31367353-35417098)x1 copy number loss See cases [RCV000141865] Chr19:31367353..35417098 [GRCh38]
Chr19:31858259..35908000 [GRCh37]
Chr19:36550099..40599840 [NCBI36]
Chr19:19q12-13.12		 pathogenic
GRCh38/hg38 19q13.11(chr19:32319651-32537584)x1 copy number loss See cases [RCV000143671] Chr19:32319651..32537584 [GRCh38]
Chr19:32810557..33028490 [GRCh37]
Chr19:37502397..37720330 [NCBI36]
Chr19:19q13.11		 uncertain significance
GRCh38/hg38 19q13.11(chr19:32312378-32535399)x1 copy number loss See cases [RCV000143640] Chr19:32312378..32535399 [GRCh38]
Chr19:32803284..33026305 [GRCh37]
Chr19:37495124..37718145 [NCBI36]
Chr19:19q13.11		 uncertain significance
GRCh38/hg38 19q11-13.11(chr19:27780238-34783942)x3 copy number gain See cases [RCV000143705] Chr19:27780238..34783942 [GRCh38]
Chr19:28271146..35274846 [GRCh37]
Chr19:32962986..39966686 [NCBI36]
Chr19:19q11-13.11		 uncertain significance
GRCh38/hg38 19p13.2-q13.31(chr19:11227942-44626354)x3 copy number gain See cases [RCV000133888] Chr19:11227942..44626354 [GRCh38]
Chr19:11338618..45129651 [GRCh37]
Chr19:11199618..49821491 [NCBI36]
Chr19:19p13.2-q13.31		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:679
Count of miRNA genes:545
Interacting mature miRNAs:609
Transcripts:ENST00000581176, ENST00000592680, ENST00000595727
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 1 17 2 6 2 1 2 13 1 197 12 1
Low 1148 1375 1309 319 1082 191 2089 652 3020 274 1131 1305 138 649 1308 4
Below cutoff 1237 1477 384 290 745 260 2158 1458 664 139 116 275 31 546 1401

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000592680
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1932,390,050 - 32,405,560 (-)Ensembl
RefSeq Acc Id: NR_046201
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381932,390,050 - 32,405,539 (-)NCBI
T2T-CHM13v2.01934,908,692 - 34,924,194 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein AAH00922 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC DPY19L3-DT COSMIC
Ensembl Genes ENSG00000267213 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000592680 ENTREZGENE
GTEx ENSG00000267213 GTEx
HGNC ID HGNC:55307 ENTREZGENE
Human Proteome Map DPY19L3-DT Human Proteome Map
NCBI Gene LOC400684 ENTREZGENE
RNAcentral URS000075A922 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-10-19 DPY19L3-DT  DPY19L3 divergent transcript  AC007773.1  novel transcript, antisense to DPY19L3  Symbol and/or name change 19259463 PROVISIONAL
2020-06-25 AC007773.1  novel transcript, antisense to DPY19L3  LOC400684  uncharacterized LOC400684  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC400684  uncharacterized LOC400684  AC007773.1  novel transcript, antisense to DPY19L3  Symbol and/or name change 5135510 APPROVED