LINC02533 (long intergenic non-protein coding RNA 2533) - Rat Genome Database

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Gene: LINC02533 (long intergenic non-protein coding RNA 2533) Homo sapiens
Analyze
Symbol: LINC02533
Name: long intergenic non-protein coding RNA 2533
RGD ID: 12910410
HGNC Page HGNC:53566
Description: INTERACTS WITH aflatoxin B1; cadmium atom; sodium arsenite
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
GRCh3864,488,798 - 4,495,771 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl64,488,720 - 4,509,528 (+)EnsemblGRCh38hg38GRCh38
GRCh3764,489,032 - 4,496,005 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map6p25.1NCBI
CHM1_164,490,590 - 4,498,642 (+)NCBICHM1_1
T2T-CHM13v2.064,357,719 - 4,364,687 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model



  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
LINC02533Humanaflatoxin B1 decreases methylationEXP 6480464Aflatoxin B1 results in decreased methylation of LINC02533 polyA tailCTDPMID:30157460
LINC02533Humancadmium atom increases expressionEXP 6480464Cadmium results in increased expression of LINC02533 mRNACTDPMID:33559965
LINC02533Humansodium arsenite increases expressionEXP 6480464sodium arsenite results in increased expression of LINC02533 mRNACTDPMID:38568856

PMID:10737800   PMID:14702039   PMID:16344560  



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Variants in LINC02533
1 total Variants

1 to 10 of 30 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
GRCh38/hg38 6p25.3-25.1(chr6:163083-6062800)x1 copy number loss See cases [RCV000050686] Chr6:163083..6062800 [GRCh38]
Chr6:163083..6063033 [GRCh37]
Chr6:108083..6008032 [NCBI36]
Chr6:6p25.3-25.1
pathogenic
GRCh38/hg38 6p25.3-22.3(chr6:106431-18360595)x3 copy number gain See cases [RCV000051869] Chr6:106431..18360595 [GRCh38]
Chr6:106431..18360826 [GRCh37]
Chr6:51431..18468805 [NCBI36]
Chr6:6p25.3-22.3
pathogenic
GRCh38/hg38 6p25.3-23(chr6:389423-13474956)x3 copy number gain See cases [RCV000051896] Chr6:389423..13474956 [GRCh38]
Chr6:389423..13475188 [GRCh37]
Chr6:334423..13583167 [NCBI36]
Chr6:6p25.3-23
pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:107682-4978781)x1 copy number loss See cases [RCV000052159] Chr6:107682..4978781 [GRCh38]
Chr6:107682..4979015 [GRCh37]
Chr6:52682..4924014 [NCBI36]
Chr6:6p25.3-25.1
pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:162883-5979198)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052160]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052160]|See cases [RCV000052160] Chr6:162883..5979198 [GRCh38]
Chr6:162883..5979431 [GRCh37]
Chr6:107883..5924430 [NCBI36]
Chr6:6p25.3-25.1
pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:163083-5875402)x1 copy number loss See cases [RCV000052161] Chr6:163083..5875402 [GRCh38]
Chr6:163083..5875635 [GRCh37]
Chr6:108083..5820634 [NCBI36]
Chr6:6p25.3-25.1
pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:164633-6284237)x1 copy number loss See cases [RCV000052163] Chr6:164633..6284237 [GRCh38]
Chr6:164633..6284470 [GRCh37]
Chr6:109633..6229469 [NCBI36]
Chr6:6p25.3-25.1
pathogenic
GRCh38/hg38 6p25.3-25.1(chr6:164633-5823601)x1 copy number loss See cases [RCV000052164] Chr6:164633..5823601 [GRCh38]
Chr6:164633..5823834 [GRCh37]
Chr6:109633..5768833 [NCBI36]
Chr6:6p25.3-25.1
pathogenic
GRCh38/hg38 6p25.3-24.3(chr6:165675-9036034)x1 copy number loss See cases [RCV000052165] Chr6:165675..9036034 [GRCh38]
Chr6:165675..9036267 [GRCh37]
Chr6:110675..8981266 [NCBI36]
Chr6:6p25.3-24.3
pathogenic
GRCh38/hg38 6p25.3-24.1(chr6:164360-13339881)x3 copy number gain See cases [RCV000134022] Chr6:164360..13339881 [GRCh38]
Chr6:164360..13340113 [GRCh37]
Chr6:109360..13448092 [NCBI36]
Chr6:6p25.3-24.1
pathogenic
1 to 10 of 30 rows

Predicted Target Of
Summary Value
Count of predictions:163
Count of miRNA genes:153
Interacting mature miRNAs:162
Transcripts:ENST00000563079
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.


The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
2289408BW324_HBody weight QTL 324 (human)3.150.0001Body fat amount6120803913Human
1643418BW282_HBody Weight QTL 282 (human)2.070.001Body weight6119321359Human
2289435BMD4_HBone mineral density QTL 4 (human)3.150.0001Bone mineral density6120803913Human
2292824PRSTS5_HProstate tumor susceptibility QTL 5 (human)Prostate tumor susceptibility6119232373Human
2289320BW390_HBody weight QTL 390 (human)2.13Body weightBMI6119321359Human
1643495BW291_HBody Weight QTL 291 (human)2.13Body weightBMI6119321359Human




adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
614 1060 1456 1159 2565 797 1240 4 228 586 138 1281 3100 2848 47 1806 391 1068 945 100



Ensembl Acc Id: ENST00000563079
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,491,803 - 4,495,769 (+)Ensembl
Ensembl Acc Id: ENST00000673975
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,491,807 - 4,495,769 (+)Ensembl
Ensembl Acc Id: ENST00000674020
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,744 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827245
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,832 - 4,509,528 (+)Ensembl
Ensembl Acc Id: ENST00000827246
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,834 - 4,509,521 (+)Ensembl
Ensembl Acc Id: ENST00000827247
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,745 - 4,494,793 (+)Ensembl
Ensembl Acc Id: ENST00000827248
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,793 - 4,494,793 (+)Ensembl
Ensembl Acc Id: ENST00000827249
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,720 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827250
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,763 - 4,494,614 (+)Ensembl
Ensembl Acc Id: ENST00000827251
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,762 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827252
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,762 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827253
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,774 - 4,494,616 (+)Ensembl
Ensembl Acc Id: ENST00000827254
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,778 - 4,494,614 (+)Ensembl
Ensembl Acc Id: ENST00000827255
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,778 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827256
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,778 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827257
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,795 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827258
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,795 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827259
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,795 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827260
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,795 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827261
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,798 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827262
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,802 - 4,495,245 (+)Ensembl
Ensembl Acc Id: ENST00000827263
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,823 - 4,495,245 (+)Ensembl
Ensembl Acc Id: ENST00000827264
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,788 - 4,494,614 (+)Ensembl
Ensembl Acc Id: ENST00000827265
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,806 - 4,494,614 (+)Ensembl
Ensembl Acc Id: ENST00000827266
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,806 - 4,494,614 (+)Ensembl
Ensembl Acc Id: ENST00000827267
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,808 - 4,494,614 (+)Ensembl
Ensembl Acc Id: ENST00000827268
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,808 - 4,494,614 (+)Ensembl
Ensembl Acc Id: ENST00000827269
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,820 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827270
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,490,291 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827271
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,490,291 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827272
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,490,291 - 4,494,613 (+)Ensembl
Ensembl Acc Id: ENST00000827273
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,489,806 - 4,490,863 (+)Ensembl
Ensembl Acc Id: ENST00000827274
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl64,488,829 - 4,489,609 (+)Ensembl
RefSeq Acc Id: NR_149117
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3864,488,798 - 4,495,771 (+)NCBI
T2T-CHM13v2.064,357,719 - 4,364,687 (+)NCBI
Sequence:


1 to 9 of 9 rows
Database
Acc Id
Source(s)
COSMIC LINC02533 COSMIC
Ensembl Genes ENSG00000260239 Ensembl
GTEx ENSG00000260239 GTEx
HGNC ID HGNC:53566 ENTREZGENE
Human Proteome Map LINC02533 Human Proteome Map
NCBI Gene LINC02533 ENTREZGENE
RNAcentral URS00002BB5A0 RNACentral
  URS0000BC4576 RNACentral
  URS000199F702 RNACentral
1 to 9 of 9 rows