LINC02024 (long intergenic non-protein coding RNA 2024) - Rat Genome Database

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Gene: LINC02024 (long intergenic non-protein coding RNA 2024) Homo sapiens
Analyze
Symbol: LINC02024
Name: long intergenic non-protein coding RNA 2024
RGD ID: 11571208
HGNC Page HGNC:52859
Description:
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
GRCh383117,678,693 - 117,690,925 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3117,678,693 - 117,691,005 (-)EnsemblGRCh38hg38GRCh38
GRCh373117,397,540 - 117,409,772 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3q13.32NCBI
CHM1_13117,361,281 - 117,376,482 (-)NCBICHM1_1
T2T-CHM13v2.03120,398,445 - 120,410,666 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics

Variants

.
Variants in LINC02024
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q13.31-21.2(chr3:114122562-124532374)x1 copy number loss See cases [RCV000142009] Chr3:114122562..124532374 [GRCh38]
Chr3:113841409..124251221 [GRCh37]
Chr3:115324099..125733911 [NCBI36]
Chr3:3q13.31-21.2		 pathogenic
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24		 pathogenic
GRCh38/hg38 3q13.31-21.1(chr3:115019074-122513398)x1 copy number loss See cases [RCV000135961] Chr3:115019074..122513398 [GRCh38]
Chr3:114737921..122232245 [GRCh37]
Chr3:116220611..123714935 [NCBI36]
Chr3:3q13.31-21.1		 pathogenic
GRCh38/hg38 3q13.2-13.33(chr3:112520553-120031022)x1 copy number loss See cases [RCV000142725] Chr3:112520553..120031022 [GRCh38]
Chr3:112239400..119749869 [GRCh37]
Chr3:113722090..121232559 [NCBI36]
Chr3:3q13.2-13.33		 pathogenic
GRCh38/hg38 3q13.31-13.32(chr3:114734452-118164045)x1 copy number loss See cases [RCV000143674] Chr3:114734452..118164045 [GRCh38]
Chr3:114453299..117882892 [GRCh37]
Chr3:115935989..119365582 [NCBI36]
Chr3:3q13.31-13.32		 uncertain significance
GRCh38/hg38 3q13.31-13.32(chr3:116366433-119033600)x3 copy number gain See cases [RCV000138196] Chr3:116366433..119033600 [GRCh38]
Chr3:116085280..118752447 [GRCh37]
Chr3:117567970..120235137 [NCBI36]
Chr3:3q13.31-13.32		 uncertain significance
GRCh38/hg38 3q13.2-21.3(chr3:112620977-128734134)x1 copy number loss See cases [RCV000139033] Chr3:112620977..128734134 [GRCh38]
Chr3:112339824..128452977 [GRCh37]
Chr3:113822514..129935667 [NCBI36]
Chr3:3q13.2-21.3		 pathogenic
GRCh38/hg38 3q13.31-13.32(chr3:117255116-117844958)x1 copy number loss See cases [RCV000141018] Chr3:117255116..117844958 [GRCh38]
Chr3:116973963..117563805 [GRCh37]
Chr3:118456653..119046495 [NCBI36]
Chr3:3q13.31-13.32		 benign
GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1 copy number loss See cases [RCV000051543] Chr3:93886671..123216683 [GRCh38]
Chr3:93605515..122935530 [GRCh37]
Chr3:95088205..124418220 [NCBI36]
Chr3:3q11.1-21.1		 pathogenic
GRCh38/hg38 3q11.1-21.2(chr3:93979547-124774010)x1 copy number loss Chromosome 3q13.31 deletion syndrome [RCV003327614] Chr3:93979547..124774010 [GRCh38]
Chr3:3q11.1-21.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:211
Count of miRNA genes:202
Interacting mature miRNAs:209
Transcripts:ENST00000462528, ENST00000493545, ENST00000496994
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 entire extraembryonic component
High
Medium 248
Low 3 6 11 2 20 2 27 12 56 3 148 87 6 1
Below cutoff 454 241 443 38 212 29 605 189 1734 85 439 608 19 124 312 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000462528
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3117,682,914 - 117,688,861 (-)Ensembl
RefSeq Acc Id: ENST00000493545
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3117,678,693 - 117,690,955 (-)Ensembl
RefSeq Acc Id: ENST00000496994
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3117,682,914 - 117,690,955 (-)Ensembl
RefSeq Acc Id: ENST00000656611
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3117,688,219 - 117,690,975 (-)Ensembl
RefSeq Acc Id: ENST00000659069
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3117,678,698 - 117,691,005 (-)Ensembl
RefSeq Acc Id: ENST00000660985
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3117,678,698 - 117,690,989 (-)Ensembl
RefSeq Acc Id: ENST00000662843
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3117,678,698 - 117,690,961 (-)Ensembl
RefSeq Acc Id: ENST00000665283
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3117,678,697 - 117,690,986 (-)Ensembl
RefSeq Acc Id: ENST00000665643
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3117,678,693 - 117,690,955 (-)Ensembl
RefSeq Acc Id: NR_146652
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383117,678,693 - 117,690,925 (-)NCBI
T2T-CHM13v2.03120,398,445 - 120,410,666 (-)NCBI
Sequence:
Promoters
RGD ID:15095667
Promoter ID:EPDNEWNC_H488
Type:initiation region
Name:LINC02024_1
Description:long intergenic non-protein coding RNA 2024 [Source:HGNCSymbol;Acc:HGNC:52859]
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
GRCh383117,688,897 - 117,688,957EPDNEWNC
RGD ID:15095652
Promoter ID:EPDNEWNC_H489
Type:initiation region
Name:LINC02024_2
Description:long intergenic non-protein coding RNA 2024 [Source:HGNCSymbol;Acc:HGNC:52859]
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
GRCh383117,690,953 - 117,691,013EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC02024 COSMIC
Ensembl Genes ENSG00000241213 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000493545 ENTREZGENE
GTEx ENSG00000241213 GTEx
HGNC ID HGNC:52859 ENTREZGENE
Human Proteome Map LINC02024 Human Proteome Map
NCBI Gene LINC02024 ENTREZGENE
RNAcentral URS0000BC44F8 RNACentral