LINC01409 (long intergenic non-protein coding RNA 1409) - 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: LINC01409 (long intergenic non-protein coding RNA 1409) Homo sapiens
Analyze
Symbol: LINC01409
Name: long intergenic non-protein coding RNA 1409
RGD ID: 14400148
HGNC Page HGNC:50701
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
GRCh381778,798 - 810,065 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1778,747 - 810,065 (+)EnsemblGRCh38hg38GRCh38
Cytogenetic Map1p36.33NCBI
CHM1_11701,345 - 733,071 (+)NCBICHM1_1
T2T-CHM13v2.01205,335 - 238,971 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p36.33-36.23(chr1:629025-8537745)x1 copy number loss See cases [RCV000051993] Chr1:629025..8537745 [GRCh38]
Chr1:564405..8597804 [GRCh37]
Chr1:554268..8520391 [NCBI36]
Chr1:1p36.33-36.23		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:629044-3346226)x1 copy number loss See cases [RCV000051994] Chr1:629044..3346226 [GRCh38]
Chr1:564424..3262790 [GRCh37]
Chr1:554287..3252650 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.31(chr1:629044-7008678)x1 copy number loss See cases [RCV000051995] Chr1:629044..7008678 [GRCh38]
Chr1:564424..7068738 [GRCh37]
Chr1:554287..6991325 [NCBI36]
Chr1:1p36.33-36.31		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:778698-4898439)x1 copy number loss See cases [RCV000140164] Chr1:778698..4898439 [GRCh38]
Chr1:714078..4958499 [GRCh37]
Chr1:703941..4858359 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-36.32(chr1:792758-5006311)x3 copy number gain See cases [RCV000051779] Chr1:792758..5006311 [GRCh38]
Chr1:728138..5066371 [GRCh37]
Chr1:718001..4966231 [NCBI36]
Chr1:1p36.33-36.32		 pathogenic
GRCh38/hg38 1p36.33-35.1(chr1:99125-34026935)x3 copy number gain Trisomy 12p [RCV003447845] Chr1:99125..34026935 [GRCh38]
Chr1:1p36.33-35.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2309
Count of miRNA genes:966
Interacting mature miRNAs:1163
Transcripts:ENST00000358533, ENST00000412115, ENST00000429505, ENST00000434264, ENST00000443772, ENST00000457084, ENST00000585745, ENST00000585768, ENST00000585826, ENST00000586288, ENST00000586928, ENST00000587126, ENST00000587530, ENST00000588951, ENST00000589531, ENST00000589899, ENST00000590848, ENST00000591440, ENST00000591702, ENST00000592547, ENST00000593022, ENST00000609830
Prediction methods:Microtar, 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 31 5 7 4
Low 1667 1158 1245 331 961 196 3057 673 2529 221 1325 1408 147 591 1860 4
Below cutoff 763 1818 471 284 946 261 1298 1513 1179 195 116 195 23 613 928

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000412115
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,747 - 810,063 (+)Ensembl
RefSeq Acc Id: ENST00000429505
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,760 - 805,270 (+)Ensembl
RefSeq Acc Id: ENST00000434264
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,770 - 784,690 (+)Ensembl
RefSeq Acc Id: ENST00000443772
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,972 - 808,378 (+)Ensembl
RefSeq Acc Id: ENST00000457084
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,782 - 782,191 (+)Ensembl
RefSeq Acc Id: ENST00000585745
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 795,513 (+)Ensembl
RefSeq Acc Id: ENST00000585768
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 801,876 (+)Ensembl
RefSeq Acc Id: ENST00000585826
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 784,759 (+)Ensembl
RefSeq Acc Id: ENST00000586288
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,396 - 807,321 (+)Ensembl
RefSeq Acc Id: ENST00000586928
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 786,866 (+)Ensembl
RefSeq Acc Id: ENST00000587530
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 805,270 (+)Ensembl
RefSeq Acc Id: ENST00000588951
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 809,729 (+)Ensembl
RefSeq Acc Id: ENST00000589531
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 807,314 (+)Ensembl
RefSeq Acc Id: ENST00000589899
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,930 - 784,655 (+)Ensembl
RefSeq Acc Id: ENST00000590848
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 804,832 (+)Ensembl
RefSeq Acc Id: ENST00000591440
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 805,127 (+)Ensembl
RefSeq Acc Id: ENST00000591702
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1785,800 - 787,672 (+)Ensembl
RefSeq Acc Id: ENST00000592547
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 784,977 (+)Ensembl
RefSeq Acc Id: ENST00000593022
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1784,370 - 806,459 (+)Ensembl
RefSeq Acc Id: ENST00000609830
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,937 - 784,429 (+)Ensembl
RefSeq Acc Id: ENST00000651411
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,849 - 805,272 (+)Ensembl
RefSeq Acc Id: ENST00000655384
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1803,836 - 806,580 (+)Ensembl
RefSeq Acc Id: ENST00000655765
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,747 - 805,994 (+)Ensembl
RefSeq Acc Id: ENST00000656571
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,802 - 810,057 (+)Ensembl
RefSeq Acc Id: ENST00000657896
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,760 - 810,062 (+)Ensembl
RefSeq Acc Id: ENST00000658648
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,796 - 810,062 (+)Ensembl
RefSeq Acc Id: ENST00000665719
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,812 - 810,065 (+)Ensembl
RefSeq Acc Id: ENST00000665867
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,809 - 787,186 (+)Ensembl
RefSeq Acc Id: ENST00000666217
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,812 - 810,057 (+)Ensembl
RefSeq Acc Id: ENST00000667728
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1803,934 - 807,435 (+)Ensembl
RefSeq Acc Id: ENST00000669749
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,809 - 810,047 (+)Ensembl
RefSeq Acc Id: ENST00000670700
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1778,758 - 810,062 (+)Ensembl
RefSeq Acc Id: NR_187359
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381778,798 - 810,065 (+)NCBI
T2T-CHM13v2.01205,335 - 238,971 (+)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC LINC01409 COSMIC
Ensembl Genes ENSG00000237491 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000665719 ENTREZGENE
GTEx ENSG00000237491 GTEx
HGNC ID HGNC:50701 ENTREZGENE
Human Proteome Map LINC01409 Human Proteome Map
NCBI Gene LINC01409 ENTREZGENE
RNAcentral URS00026A1BF4 RNACentral