LINC01015 (long intergenic non-protein coding RNA 1015) - 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: LINC01015 (long intergenic non-protein coding RNA 1015) Homo sapiens
Analyze
Symbol: LINC01015
Name: long intergenic non-protein coding RNA 1015
RGD ID: 7248225
HGNC Page HGNC:48988
Description: INTERACTS WITH 4,4'-sulfonyldiphenol
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
GRCh38629,529,406 - 29,533,568 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl629,528,721 - 29,533,665 (+)EnsemblGRCh38hg38GRCh38
GRCh37629,497,183 - 29,501,345 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map6p22.1NCBI
HuRef629,304,352 - 29,308,514 (+)NCBIHuRef
CHM1_1629,499,307 - 29,503,469 (+)NCBICHM1_1
T2T-CHM13v2.0629,404,068 - 29,408,230 (+)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:14702039   PMID:16344560   PMID:16751776  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6p25.2-21.33(chr6:3224310-30657190)x3 copy number gain See cases [RCV000138956] Chr6:3224310..30657190 [GRCh38]
Chr6:3224544..30624967 [GRCh37]
Chr6:3169543..30732946 [NCBI36]
Chr6:6p25.2-21.33		 pathogenic
GRCh38/hg38 6p22.1(chr6:28763187-29769828)x3 copy number gain See cases [RCV000141858] Chr6:28763187..29769828 [GRCh38]
Chr6:28730964..29737605 [GRCh37]
Chr6:28838943..29845584 [NCBI36]
Chr6:6p22.1		 uncertain significance
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3		 pathogenic
GRCh38/hg38 6p22.3-21.33(chr6:18120520-30767516)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]|See cases [RCV000052180] Chr6:18120520..30767516 [GRCh38]
Chr6:18120751..30735293 [GRCh37]
Chr6:18228730..30843272 [NCBI36]
Chr6:6p22.3-21.33		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:618
Count of miRNA genes:433
Interacting mature miRNAs:461
Transcripts:ENST00000434657, ENST00000445296
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
High
Medium 344
Low 1 4 1 1 4 2 1 30 5 4
Below cutoff 570 787 410 97 498 66 904 420 707 27 209 404 31 321 568

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_037179 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_037180 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_037181 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AK097713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK126097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL662826 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL662860 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX000531 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX247947 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX927223 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CD358111 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR759768 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR759770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR788300 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB050954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB052894 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000434657
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl629,529,420 - 29,533,665 (+)Ensembl
RefSeq Acc Id: ENST00000445296
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl629,529,476 - 29,532,157 (+)Ensembl
RefSeq Acc Id: ENST00000647732
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl629,529,443 - 29,533,560 (+)Ensembl
RefSeq Acc Id: ENST00000648831
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl629,528,750 - 29,533,556 (+)Ensembl
RefSeq Acc Id: ENST00000658484
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl629,528,721 - 29,531,240 (+)Ensembl
RefSeq Acc Id: NR_037179
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38629,529,406 - 29,533,568 (+)NCBI
GRCh37629,497,183 - 29,501,345 (+)NCBI
HuRef629,304,352 - 29,308,514 (+)NCBI
CHM1_1629,499,307 - 29,503,469 (+)NCBI
T2T-CHM13v2.0629,404,068 - 29,408,230 (+)NCBI
Sequence:
RefSeq Acc Id: NR_037180
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38629,529,406 - 29,533,568 (+)NCBI
GRCh37629,497,183 - 29,501,345 (+)NCBI
HuRef629,304,352 - 29,308,514 (+)NCBI
CHM1_1629,499,307 - 29,503,469 (+)NCBI
T2T-CHM13v2.0629,404,068 - 29,408,230 (+)NCBI
Sequence:
RefSeq Acc Id: NR_037181
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38629,529,406 - 29,533,568 (+)NCBI
GRCh37629,497,183 - 29,501,345 (+)NCBI
HuRef629,304,352 - 29,308,514 (+)NCBI
CHM1_1629,499,307 - 29,503,469 (+)NCBI
T2T-CHM13v2.0629,404,068 - 29,408,230 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01015 COSMIC
Ensembl Genes ENSG00000224582 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000434657 ENTREZGENE
  ENST00000648831 ENTREZGENE
GTEx ENSG00000224582 GTEx
HGNC ID HGNC:48988 ENTREZGENE
Human Proteome Map LINC01015 Human Proteome Map
NCBI Gene LINC01015 ENTREZGENE
RNAcentral URS000075AE26 RNACentral
  URS000075CB7B RNACentral
  URS000075EBA4 RNACentral