LINC00930 (long intergenic non-protein coding RNA 930) - 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: LINC00930 (long intergenic non-protein coding RNA 930) Homo sapiens
Analyze
Symbol: LINC00930
Name: long intergenic non-protein coding RNA 930
RGD ID: 7245006
HGNC Page HGNC:48620
Description: INTERACTS WITH 17beta-hydroxy-5alpha-androstan-3-one; benzo[a]pyrene
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP11-304N14.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381592,567,818 - 92,572,263 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1592,567,817 - 92,574,529 (-)EnsemblGRCh38hg38GRCh38
GRCh371593,111,048 - 93,115,493 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera1569,522,910 - 69,527,434 (-)NCBICelera
Cytogenetic Map15q26.1NCBI
HuRef1569,248,084 - 69,252,530 (-)NCBIHuRef
CHM1_11592,952,116 - 92,956,561 (-)NCBICHM1_1
T2T-CHM13v2.01590,330,259 - 90,334,704 (-)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 15q25.2-26.3(chr15:83711377-101843270)x3 copy number gain See cases [RCV000135858] Chr15:83711377..101843270 [GRCh38]
Chr15:84380129..102383473 [GRCh37]
Chr15:82171133..100200996 [NCBI36]
Chr15:15q25.2-26.3		 pathogenic
GRCh38/hg38 15q25.3-26.3(chr15:87904735-101843270)x3 copy number gain See cases [RCV000135568] Chr15:87904735..101843270 [GRCh38]
Chr15:88447966..102383473 [GRCh37]
Chr15:86248970..100200996 [NCBI36]
Chr15:15q25.3-26.3		 pathogenic
GRCh38/hg38 15q25.2-26.3(chr15:82859676-101810992)x3 copy number gain See cases [RCV000136849] Chr15:82859676..101810992 [GRCh38]
Chr15:83528428..102351195 [GRCh37]
Chr15:81325482..100168718 [NCBI36]
Chr15:15q25.2-26.3		 pathogenic
GRCh38/hg38 15q25.3-26.3(chr15:85826665-101920998)x4 copy number gain See cases [RCV000137264] Chr15:85826665..101920998 [GRCh38]
Chr15:86369896..102461201 [GRCh37]
Chr15:84170900..100278724 [NCBI36]
Chr15:15q25.3-26.3		 pathogenic
GRCh38/hg38 15q25.3-26.3(chr15:85397539-101888909)x3 copy number gain See cases [RCV000141899] Chr15:85397539..101888909 [GRCh38]
Chr15:85940770..102429112 [GRCh37]
Chr15:83741774..100246635 [NCBI36]
Chr15:15q25.3-26.3		 pathogenic
GRCh38/hg38 15q23-26.3(chr15:72154949-101920998)x3 copy number gain See cases [RCV000143019] Chr15:72154949..101920998 [GRCh38]
Chr15:72447290..102461201 [GRCh37]
Chr15:70234344..100278724 [NCBI36]
Chr15:15q23-26.3		 pathogenic
GRCh38/hg38 15q22.2-26.3(chr15:59828460-101920998)x3 copy number gain See cases [RCV000142915] Chr15:59828460..101920998 [GRCh38]
Chr15:60120659..102461201 [GRCh37]
Chr15:57907951..100278724 [NCBI36]
Chr15:15q22.2-26.3		 pathogenic
GRCh38/hg38 15q26.1-26.3(chr15:88676575-98364743)x3 copy number gain See cases [RCV000142727] Chr15:88676575..98364743 [GRCh38]
Chr15:89219806..98907972 [GRCh37]
Chr15:87020810..96725495 [NCBI36]
Chr15:15q26.1-26.3		 pathogenic
GRCh38/hg38 15q24.2-26.3(chr15:75307767-101723215)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052346]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052346]|See cases [RCV000052346] Chr15:75307767..101723215 [GRCh38]
Chr15:75600108..102263418 [GRCh37]
Chr15:73387161..100080941 [NCBI36]
Chr15:15q24.2-26.3		 pathogenic
GRCh38/hg38 15q24.3-26.3(chr15:77543797-101843411)x3 copy number gain See cases [RCV000052347] Chr15:77543797..101843411 [GRCh38]
Chr15:77836139..102383614 [GRCh37]
Chr15:75623194..100201137 [NCBI36]
Chr15:15q24.3-26.3		 pathogenic
GRCh38/hg38 15q25.2-26.3(chr15:84169153-101904929)x3 copy number gain See cases [RCV000052352] Chr15:84169153..101904929 [GRCh38]
Chr15:84837905..102445132 [GRCh37]
Chr15:82628909..100262655 [NCBI36]
Chr15:15q25.2-26.3		 pathogenic
GRCh38/hg38 15q26.1-26.3(chr15:89679237-101978958)x3 copy number gain See cases [RCV000052354] Chr15:89679237..101978958 [GRCh38]
Chr15:90222468..102519161 [GRCh37]
Chr15:88023472..100336684 [NCBI36]
Chr15:15q26.1-26.3		 pathogenic
GRCh38/hg38 15q26.1(chr15:92170113-93438995)x1 copy number loss See cases [RCV000053225] Chr15:92170113..93438995 [GRCh38]
Chr15:92713343..93982224 [GRCh37]
Chr15:90514347..91783228 [NCBI36]
Chr15:15q26.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:367
Count of miRNA genes:317
Interacting mature miRNAs:342
Transcripts:ENST00000554542, ENST00000557075
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
High
Medium 13 55 9 2 1 47 49 10 13 483 127 8 47
Low 1866 636 942 160 329 26 1854 1396 1680 83 661 1199 133 203 1403
Below cutoff 422 2008 558 328 812 311 2172 696 1889 164 215 124 20 914 1293

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_021493 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC091580 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI149645 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK093148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL045331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB045163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB061727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB337836 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ572600 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ579282 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ579770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ582019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ582200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ583468 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ583920 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ584430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ584431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ586969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ591924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ593065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ593960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ594661 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ595207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ600577 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DQ601144 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000554542
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1592,567,819 - 92,574,517 (-)Ensembl
RefSeq Acc Id: ENST00000557075
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1592,567,820 - 92,571,697 (-)Ensembl
RefSeq Acc Id: ENST00000653070
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1592,567,817 - 92,574,519 (-)Ensembl
RefSeq Acc Id: ENST00000654017
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1592,567,817 - 92,574,529 (-)Ensembl
RefSeq Acc Id: NR_021493
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381592,567,818 - 92,572,263 (-)NCBI
GRCh371593,111,048 - 93,115,493 (-)NCBI
HuRef1569,248,084 - 69,252,530 (-)NCBI
CHM1_11592,952,116 - 92,956,561 (-)NCBI
T2T-CHM13v2.01590,330,259 - 90,334,704 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC00930 COSMIC
Ensembl Genes ENSG00000258647 Ensembl
GTEx ENSG00000258647 GTEx
HGNC ID HGNC:48620 ENTREZGENE
Human Proteome Map LINC00930 Human Proteome Map
NCBI Gene LINC00930 ENTREZGENE
RNAcentral URS000075B26A RNACentral