LINC01476 (long intergenic non-protein coding RNA 1476) - Rat Genome Database

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Gene: LINC01476 (long intergenic non-protein coding RNA 1476) Homo sapiens
Analyze
Symbol: LINC01476
Name: long intergenic non-protein coding RNA 1476
RGD ID: 8695308
HGNC Page HGNC:51117
Description: INTERACTS WITH Aflatoxin B2 alpha
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
GRCh381759,430,869 - 59,526,857 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1759,422,088 - 59,526,946 (-)EnsemblGRCh38hg38GRCh38
GRCh371757,508,230 - 57,604,218 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map17q22-q23.1NCBI
HuRef1752,889,406 - 52,964,420 (-)NCBIHuRef
CHM1_11757,594,686 - 57,669,547 (-)NCBICHM1_1
T2T-CHM13v2.01760,299,012 - 60,395,027 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:16344560  


Genomics

Variants

.
Variants in LINC01476
7 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_110813.1(LINC01476):n.494+20449G>T single nucleotide variant Lung cancer [RCV000100577] Chr17:59482530 [GRCh38]
Chr17:57559891 [GRCh37]
Chr17:17q22		 uncertain significance
GRCh38/hg38 17q22-23.1(chr17:59481220-59756756)x1 copy number loss See cases [RCV000135625] Chr17:59481220..59756756 [GRCh38]
Chr17:57558581..57834117 [GRCh37]
Chr17:54913363..55188899 [NCBI36]
Chr17:17q22-23.1		 likely pathogenic|uncertain significance
GRCh38/hg38 17q22-23.1(chr17:59151820-59547491)x3 copy number gain See cases [RCV000136959] Chr17:59151820..59547491 [GRCh38]
Chr17:57229181..57624852 [GRCh37]
Chr17:54583963..54979634 [NCBI36]
Chr17:17q22-23.1		 benign
GRCh38/hg38 17q23.1-25.1(chr17:36449220-75053130)x3 copy number gain See cases [RCV000137437] Chr17:36449220..75053130 [GRCh38]
Chr17:57595736..73049225 [GRCh37]
Chr17:54950518..70560820 [NCBI36]
Chr17:17q23.1-25.1		 pathogenic
GRCh38/hg38 17q22-23.1(chr17:57418806-59735464)x1 copy number loss See cases [RCV000140211] Chr17:57418806..59735464 [GRCh38]
Chr17:55496167..57812825 [GRCh37]
Chr17:52851166..55167607 [NCBI36]
Chr17:17q22-23.1		 pathogenic
GRCh38/hg38 17q22-23.1(chr17:59151705-59547602)x3 copy number gain See cases [RCV000139556] Chr17:59151705..59547602 [GRCh38]
Chr17:57229066..57624963 [GRCh37]
Chr17:54583848..54979745 [NCBI36]
Chr17:17q22-23.1		 likely benign
GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3 copy number gain See cases [RCV000050957] Chr17:36449220..68170214 [GRCh38]
Chr17:48563237..65936105 [GRCh37]
Chr17:45918236..63677950 [NCBI36]
Chr17:17q21.33-24.2		 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
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:332
Count of miRNA genes:296
Interacting mature miRNAs:307
Transcripts:ENST00000577478, ENST00000584262
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 22
Low 1 3 1 3 1 1 1 820 2 34 4 1
Below cutoff 99 177 129 47 98 41 296 107 951 41 373 115 7 51 203

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000577478
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1759,430,670 - 59,526,872 (-)Ensembl
RefSeq Acc Id: ENST00000584262
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1759,429,143 - 59,526,946 (-)Ensembl
RefSeq Acc Id: ENST00000654551
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1759,430,019 - 59,526,857 (-)Ensembl
RefSeq Acc Id: ENST00000660347
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1759,429,343 - 59,526,856 (-)Ensembl
RefSeq Acc Id: ENST00000665301
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1759,422,088 - 59,526,851 (-)Ensembl
RefSeq Acc Id: ENST00000665757
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1759,429,153 - 59,526,851 (-)Ensembl
RefSeq Acc Id: ENST00000670915
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1759,429,158 - 59,526,860 (-)Ensembl
RefSeq Acc Id: ENST00000671404
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1759,429,163 - 59,526,649 (-)Ensembl
RefSeq Acc Id: ENST00000702234
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1759,424,907 - 59,526,857 (-)Ensembl
RefSeq Acc Id: ENST00000702848
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1759,429,141 - 59,526,857 (-)Ensembl
RefSeq Acc Id: NR_110813
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381759,430,869 - 59,526,857 (-)NCBI
CHM1_11757,573,554 - 57,669,458 (-)NCBI
T2T-CHM13v2.01760,299,012 - 60,395,027 (-)NCBI
Sequence:
Promoters
RGD ID:15097079
Promoter ID:EPDNEWNC_H1910
Type:initiation region
Name:LINC01476_1
Description:long intergenic non-protein coding RNA 1476 [Source:HGNCSymbol;Acc:HGNC:51117]
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
GRCh381759,526,857 - 59,526,917EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01476 COSMIC
Ensembl Genes ENSG00000265313 Ensembl
GTEx ENSG00000265313 GTEx
HGNC ID HGNC:51117 ENTREZGENE
Human Proteome Map LINC01476 Human Proteome Map
NCBI Gene LINC01476 ENTREZGENE
RNAcentral URS000075E0FB RNACentral