LINC01973 (long intergenic non-protein coding RNA 1973) - 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: LINC01973 (long intergenic non-protein coding RNA 1973) Homo sapiens
Analyze
Symbol: LINC01973
Name: long intergenic non-protein coding RNA 1973
RGD ID: 1603144
HGNC Page HGNC:52800
Description: INTERACTS WITH benzo[a]pyrene; malathion
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: FLJ45079; FLJ46474
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381777,879,001 - 77,884,087 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1777,877,330 - 77,884,119 (-)EnsemblGRCh38hg38GRCh38
GRCh371775,875,083 - 75,880,169 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361773,386,704 - 73,391,764 (-)NCBINCBI36Build 36hg18NCBI36
Celera1772,470,678 - 72,475,764 (-)NCBICelera
Cytogenetic Map17q25.3NCBI
HuRef1771,298,947 - 71,304,034 (-)NCBIHuRef
CHM1_11775,940,085 - 75,945,178 (-)NCBICHM1_1
T2T-CHM13v2.01778,772,685 - 78,777,770 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Genomics

Variants

.
Variants in LINC01973
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q24.3-25.3(chr17:69916435-83102552)x3 copy number gain See cases [RCV000143342] Chr17:69916435..83102552 [GRCh38]
Chr17:67912576..81048189 [GRCh37]
Chr17:65424171..78653717 [NCBI36]
Chr17:17q24.3-25.3		 pathogenic
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3		 pathogenic
GRCh38/hg38 17q24.3-25.3(chr17:69209079-83086677)x3 copy number gain See cases [RCV000052486] Chr17:69209079..83086677 [GRCh38]
Chr17:67205220..81044553 [GRCh37]
Chr17:64716815..78637842 [NCBI36]
Chr17:17q24.3-25.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1827
Count of miRNA genes:832
Interacting mature miRNAs:976
Transcripts:ENST00000374983
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.

Markers in Region
D17S615  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371775,874,810 - 75,874,936UniSTSGRCh37
Build 361773,386,405 - 73,386,531RGDNCBI36
Celera1772,470,405 - 72,470,531RGD
Cytogenetic Map17q25.3UniSTS
HuRef1771,298,674 - 71,298,800UniSTS


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
High
Medium 1
Low 3 5 3 16 2 4 1 9 2
Below cutoff 822 1539 615 117 1115 48 1463 590 2280 39 534 614 73 484 977

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000374983
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1777,879,027 - 77,884,087 (-)Ensembl
RefSeq Acc Id: ENST00000664715
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1777,877,330 - 77,884,119 (-)Ensembl
RefSeq Acc Id: NR_028337
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381777,879,001 - 77,884,087 (-)NCBI
GRCh371775,875,083 - 75,880,169 (-)RGD
Celera1772,470,678 - 72,475,764 (-)RGD
HuRef1771,298,947 - 71,304,034 (-)ENTREZGENE
CHM1_11775,940,085 - 75,945,178 (-)NCBI
T2T-CHM13v2.01778,772,685 - 78,777,770 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein BAC86792 (Get FASTA)   NCBI Sequence Viewer  
  BAC87388 (Get FASTA)   NCBI Sequence Viewer  
  EAW89479 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC LINC01973 COSMIC
Ensembl Genes ENSG00000204283 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000374983 ENTREZGENE
GTEx ENSG00000204283 GTEx
HGNC ID HGNC:52800 ENTREZGENE
Human Proteome Map LINC01973 Human Proteome Map
NCBI Gene 400624 ENTREZGENE
RNAcentral URS000075E1E4 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-12-20 LINC01973  long intergenic non-protein coding RNA 1973  FLJ45079  FLJ45079 protein  Symbol and/or name change 5135510 APPROVED