LINC01484 (long intergenic non-protein coding RNA 1484) - 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: LINC01484 (long intergenic non-protein coding RNA 1484) Homo sapiens
Analyze
Symbol: LINC01484
Name: long intergenic non-protein coding RNA 1484
RGD ID: 8695849
HGNC Page HGNC:51136
Description: INTERACTS WITH aflatoxin B1; lipopolysaccharide; S-(1,2-dichlorovinyl)-L-cysteine
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
GRCh385173,707,599 - 173,746,209 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5173,707,614 - 173,746,279 (-)EnsemblGRCh38hg38GRCh38
GRCh375173,134,602 - 173,173,212 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q35.2NCBI
HuRef5168,231,487 - 168,237,534 (-)NCBIHuRef
CHM1_15172,568,319 - 172,574,359 (-)NCBICHM1_1
T2T-CHM13v2.05174,247,726 - 174,286,375 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:16344560  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q33.3-35.3(chr5:156825512-181269805)x3 copy number gain See cases [RCV000133847] Chr5:156825512..181269805 [GRCh38]
Chr5:156252523..180696806 [GRCh37]
Chr5:156185101..180629412 [NCBI36]
Chr5:5q33.3-35.3		 pathogenic
GRCh38/hg38 5q34-35.3(chr5:164386701-181269805)x3 copy number gain See cases [RCV000135546] Chr5:164386701..181269805 [GRCh38]
Chr5:163813707..180696806 [GRCh37]
Chr5:163746285..180629412 [NCBI36]
Chr5:5q34-35.3		 pathogenic
GRCh38/hg38 5q35.1-35.3(chr5:169334755-181285301)x3 copy number gain See cases [RCV000141249] Chr5:169334755..181285301 [GRCh38]
Chr5:168761759..180712302 [GRCh37]
Chr5:168694337..180644908 [NCBI36]
Chr5:5q35.1-35.3		 pathogenic
GRCh38/hg38 5q35.1-35.2(chr5:173237772-176614618)x3 copy number gain See cases [RCV000142647] Chr5:173237772..176614618 [GRCh38]
Chr5:172664775..176041619 [GRCh37]
Chr5:172597381..175974225 [NCBI36]
Chr5:5q35.1-35.2		 pathogenic
GRCh38/hg38 5q32-35.3(chr5:149714592-181272151)x3 copy number gain See cases [RCV000051863] Chr5:149714592..181272151 [GRCh38]
Chr5:149094155..180699152 [GRCh37]
Chr5:149074348..180631758 [NCBI36]
Chr5:5q32-35.3		 pathogenic
GRCh38/hg38 5q33.3-35.3(chr5:160029980-181269805)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051865]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051865]|See cases [RCV000051865] Chr5:160029980..181269805 [GRCh38]
Chr5:159456987..180696806 [GRCh37]
Chr5:159389565..180629412 [NCBI36]
Chr5:5q33.3-35.3		 pathogenic
GRCh38/hg38 5q34-35.3(chr5:168689326-181269946)x3 copy number gain See cases [RCV000051866] Chr5:168689326..181269946 [GRCh38]
Chr5:168116331..180696947 [GRCh37]
Chr5:168048909..180629553 [NCBI36]
Chr5:5q34-35.3		 pathogenic
GRCh38/hg38 5q35.1-35.2(chr5:172776798-174342969)x1 copy number loss See cases [RCV000052149] Chr5:172776798..174342969 [GRCh38]
Chr5:172203801..173769972 [GRCh37]
Chr5:172136407..173702578 [NCBI36]
Chr5:5q35.1-35.2		 pathogenic
GRCh38/hg38 5q35.1-35.2(chr5:172961091-175054665)x1 copy number loss See cases [RCV000052150] Chr5:172961091..175054665 [GRCh38]
Chr5:172388094..174481668 [GRCh37]
Chr5:172320700..174414274 [NCBI36]
Chr5:5q35.1-35.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:331
Count of miRNA genes:293
Interacting mature miRNAs:309
Transcripts:ENST00000517733, ENST00000518902, ENST00000521128
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 3 3 6 3 1 1 9 7 1
Low 25 8 427 228 213 221 672 9 493 123 100 143 10 494 114 2
Below cutoff 1103 1008 1183 346 909 212 2076 723 2861 229 789 1258 138 639 1405 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000517733
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5173,707,614 - 173,746,209 (-)Ensembl
RefSeq Acc Id: ENST00000518902
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5173,709,967 - 173,746,211 (-)Ensembl
RefSeq Acc Id: ENST00000521128
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5173,710,440 - 173,719,692 (-)Ensembl
RefSeq Acc Id: ENST00000654172
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5173,710,659 - 173,746,209 (-)Ensembl
RefSeq Acc Id: ENST00000664033
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5173,708,091 - 173,746,279 (-)Ensembl
RefSeq Acc Id: ENST00000665162
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5173,708,142 - 173,714,961 (-)Ensembl
RefSeq Acc Id: ENST00000668825
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5173,708,218 - 173,746,178 (-)Ensembl
RefSeq Acc Id: ENST00000669001
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5173,708,085 - 173,746,211 (-)Ensembl
RefSeq Acc Id: ENST00000669486
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5173,708,106 - 173,719,903 (-)Ensembl
RefSeq Acc Id: NR_108027
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385173,707,599 - 173,746,209 (-)NCBI
HuRef5168,230,276 - 168,269,406 (-)NCBI
CHM1_15172,567,107 - 172,605,704 (-)NCBI
T2T-CHM13v2.05174,247,726 - 174,286,375 (-)NCBI
Sequence:
Promoters
RGD ID:15095973
Promoter ID:EPDNEWNC_H816
Type:initiation region
Name:LINC01484_2
Description:long intergenic non-protein coding RNA 1484 [Source:HGNCSymbol;Acc:HGNC:51136]
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
GRCh385173,719,727 - 173,719,787EPDNEWNC
RGD ID:15095982
Promoter ID:EPDNEWNC_H817
Type:initiation region
Name:LINC01484_1
Description:long intergenic non-protein coding RNA 1484 [Source:HGNCSymbol;Acc:HGNC:51136]
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
GRCh385173,746,220 - 173,746,280EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01484 COSMIC
Ensembl Genes ENSG00000253686 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000517733 ENTREZGENE
GTEx ENSG00000253686 GTEx
HGNC ID HGNC:51136 ENTREZGENE
Human Proteome Map LINC01484 Human Proteome Map
NCBI Gene LINC01484 ENTREZGENE
RNAcentral URS000075AC6C RNACentral