LINC01569 (long intergenic non-protein coding RNA 1569) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LINC01569 (long intergenic non-protein coding RNA 1569) Homo sapiens
Analyze
Symbol: LINC01569
Name: long intergenic non-protein coding RNA 1569
RGD ID: 9588955
HGNC Page HGNC:51380
Description: ASSOCIATED WITH Atypical behavior; intellectual disability; Rubinstein-Taybi syndrome; INTERACTS WITH bisphenol A; cisplatin; fipronil
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
GRCh38164,245,825 - 4,253,789 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl164,243,943 - 4,253,847 (-)EnsemblGRCh38hg38GRCh38
GRCh37164,295,826 - 4,303,790 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera164,502,825 - 4,510,789 (-)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef164,262,840 - 4,270,804 (-)NCBIHuRef
CHM1_1164,295,417 - 4,303,381 (-)NCBICHM1_1
T2T-CHM13v2.0164,273,152 - 4,281,119 (-)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
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:14702039   PMID:37955081  


Genomics

Variants

.
Variants in LINC01569
5 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 16p13.3-13.13(chr16:46766-11525516)x3 copy number gain See cases [RCV000133780] Chr16:46766..11525516 [GRCh38]
Chr16:96766..11619372 [GRCh37]
Chr16:36766..11526873 [NCBI36]
Chr16:16p13.3-13.13		 pathogenic
GRCh38/hg38 16p13.3(chr16:46766-4247185)x3 copy number gain See cases [RCV000136687] Chr16:46766..4247185 [GRCh38]
Chr16:96766..4297186 [GRCh37]
Chr16:36766..4237187 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3(chr16:3560564-4266796)x1 copy number loss See cases [RCV000137944] Chr16:3560564..4266796 [GRCh38]
Chr16:3610565..4316797 [GRCh37]
Chr16:3550566..4256798 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3(chr16:3820522-4668347)x1 copy number loss See cases [RCV000137768] Chr16:3820522..4668347 [GRCh38]
Chr16:3870523..4718348 [GRCh37]
Chr16:3810524..4658349 [NCBI36]
Chr16:16p13.3		 pathogenic|likely pathogenic
GRCh38/hg38 16p13.3-13.12(chr16:43732-13326806)x3 copy number gain See cases [RCV000139166] Chr16:43732..13326806 [GRCh38]
Chr16:93732..13420663 [GRCh37]
Chr16:33732..13328164 [NCBI36]
Chr16:16p13.3-13.12		 pathogenic
GRCh38/hg38 16p13.3(chr16:3726702-4644961)x3 copy number gain See cases [RCV000142504] Chr16:3726702..4644961 [GRCh38]
Chr16:3776703..4694962 [GRCh37]
Chr16:3716704..4634963 [NCBI36]
Chr16:16p13.3		 pathogenic
GRCh38/hg38 16p13.3-13.11(chr16:666662-15743104)x3 copy number gain See cases [RCV000143710] Chr16:666662..15743104 [GRCh38]
Chr16:716662..15836961 [GRCh37]
Chr16:656663..15744462 [NCBI36]
Chr16:16p13.3-13.11		 pathogenic
GRCh38/hg38 16p13.3(chr16:3710449-4644951)x3 copy number gain See cases [RCV000050956] Chr16:3710449..4644951 [GRCh38]
Chr16:3760450..4694952 [GRCh37]
Chr16:3700451..4634953 [NCBI36]
Chr16:16p13.3		 uncertain significance
GRCh38/hg38 16p13.3-13.13(chr16:23141-11296695)x3 copy number gain See cases [RCV000052367] Chr16:23141..11296695 [GRCh38]
Chr16:73141..11390552 [GRCh37]
Chr16:13141..11298053 [NCBI36]
Chr16:16p13.3-13.13		 pathogenic
GRCh38/hg38 16p13.3(chr16:2850734-7110697)x1 copy number loss See cases [RCV000053270] Chr16:2850734..7110697 [GRCh38]
Chr16:2900735..7160698 [GRCh37]
Chr16:2840736..7100699 [NCBI36]
Chr16:16p13.3		 pathogenic
NC_000016.9:g.(?_3929813)_(4387545_?)dup duplication Rubinstein-Taybi syndrome 1 [RCV000708038] Chr16:3879812..4337544 [GRCh38]
Chr16:3929813..4387545 [GRCh37]
Chr16:16p13.3		 uncertain significance
Single allele deletion Atypical behavior [RCV000677111] Chr16:4214334..4337621 [GRCh38]
Chr16:4264335..4387622 [GRCh37]
Chr16:16p13.3		 uncertain significance
NC_000016.10:g.(?_3727698)_(4802591_?)del deletion Rubinstein-Taybi syndrome [RCV000813975] Chr16:3727698..4802591 [GRCh38]
Chr16:3777699..4852592 [GRCh37]
Chr16:16p13.3		 pathogenic
NC_000016.10:g.3619617_4448281del deletion See cases [RCV003313806] Chr16:3619617..4448281 [GRCh38]
Chr16:16p13.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:922
Count of miRNA genes:616
Interacting mature miRNAs:696
Transcripts:ENST00000571970, ENST00000573042, ENST00000573268
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.


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 11 231 3 51 3 2 4 1 45 61 246
Low 2377 2522 1482 611 1640 453 4303 1983 3453 371 1379 1353 170 1186 2752 4
Below cutoff 44 458 10 8 253 8 50 206 254 2 8 9 18 36

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000571970
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,008 - 4,251,864 (-)Ensembl
RefSeq Acc Id: ENST00000573042
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,245,901 - 4,253,817 (-)Ensembl
RefSeq Acc Id: ENST00000573268
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,566 - 4,253,779 (-)Ensembl
RefSeq Acc Id: ENST00000648010
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,012 - 4,253,812 (-)Ensembl
RefSeq Acc Id: ENST00000648108
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,027 - 4,252,322 (-)Ensembl
RefSeq Acc Id: ENST00000648147
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,040 - 4,252,949 (-)Ensembl
RefSeq Acc Id: ENST00000649264
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,243,943 - 4,253,789 (-)Ensembl
RefSeq Acc Id: ENST00000650502
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,251,729 - 4,253,814 (-)Ensembl
RefSeq Acc Id: ENST00000685215
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,015 - 4,253,741 (-)Ensembl
RefSeq Acc Id: ENST00000686266
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,253,286 - 4,253,816 (-)Ensembl
RefSeq Acc Id: ENST00000687438
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,006 - 4,253,816 (-)Ensembl
RefSeq Acc Id: ENST00000687603
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,253,286 - 4,253,847 (-)Ensembl
RefSeq Acc Id: ENST00000688082
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,253,286 - 4,253,816 (-)Ensembl
RefSeq Acc Id: ENST00000689983
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,006 - 4,253,759 (-)Ensembl
RefSeq Acc Id: ENST00000690276
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,006 - 4,253,790 (-)Ensembl
RefSeq Acc Id: ENST00000701038
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,006 - 4,253,790 (-)Ensembl
RefSeq Acc Id: ENST00000701646
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,012 - 4,253,812 (-)Ensembl
RefSeq Acc Id: ENST00000701924
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl164,246,012 - 4,253,788 (-)Ensembl
RefSeq Acc Id: NR_039999
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38164,245,825 - 4,253,789 (-)NCBI
HuRef164,262,840 - 4,270,804 (-)NCBI
CHM1_1164,295,417 - 4,303,381 (-)NCBI
T2T-CHM13v2.0164,273,152 - 4,281,119 (-)NCBI
Sequence:
Promoters
RGD ID:15096978
Promoter ID:EPDNEWNC_H1804
Type:initiation region
Name:LINC01569_1
Description:long intergenic non-protein coding RNA 1569 [Source:HGNCSymbol;Acc:HGNC:51380]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38164,253,789 - 4,253,849EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01569 COSMIC
Ensembl Genes ENSG00000262468 Ensembl
GTEx ENSG00000262468 GTEx
HGNC ID HGNC:51380 ENTREZGENE
Human Proteome Map LINC01569 Human Proteome Map
NCBI Gene LINC01569 ENTREZGENE
RNAcentral URS000000B904 RNACentral