LINC00592 (long intergenic non-protein coding RNA 592)

Gene: LINC00592 (long intergenic non-protein coding RNA 592) Homo sapiens

Analyze

Symbol:

LINC00592

Name:

long intergenic non-protein coding RNA 592

RGD ID:

6482980

HGNC Page

HGNC:27474

Description:

INTERACTS WITH aflatoxin B1; Aflatoxin B2 alpha; benzo[a]pyrene

Type:

ncrna (Ensembl: lncRNA)

RefSeq Status:

VALIDATED

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	52,210,930 - 52,223,880 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	52,164,115 - 52,223,813 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	52,604,714 - 52,617,664 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Celera	12	51,407,157 - 51,420,044 (+)	NCBI		Celera
Cytogenetic Map	12	q13.13	ENTREZGENE
HuRef	12	49,637,996 - 49,650,881 (+)	ENTREZGENE		HuRef
CHM1_1	12	52,570,973 - 52,583,857 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	52,174,510 - 52,187,466 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

aflatoxin B1 (EXP)

Aflatoxin B2 alpha (EXP)

benzo[a]pyrene (EXP)

benzo[e]pyrene (EXP)

bisphenol A (EXP)

methapyrilene (EXP)

nickel atom (EXP)

References

References - curated

#	Reference Title	Reference Citation
1.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:11329013	PMID:12477932

Genomics

Variants

Variants in LINC00592
1 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3	copy number gain	See cases [RCV000139555]	Chr12:121271..133196807 [GRCh38] Chr12:282465..133773393 [GRCh37] Chr12:100698..132283466 [NCBI36] Chr12:12p13.33-q24.33	pathogenic
GRCh38/hg38 12q13.12-13.13(chr12:50633888-52851909)x1	copy number loss	See cases [RCV000140716]	Chr12:50633888..52851909 [GRCh38] Chr12:51027671..53245693 [GRCh37] Chr12:49313938..51531960 [NCBI36] Chr12:12q13.12-13.13	pathogenic
GRCh38/hg38 12q13.12-13.13(chr12:50122359-53248460)x1	copy number loss	See cases [RCV000142033]	Chr12:50122359..53248460 [GRCh38] Chr12:50516142..53642244 [GRCh37] Chr12:48802409..51928511 [NCBI36] Chr12:12q13.12-13.13	pathogenic

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	48
Count of miRNA genes:	47
Interacting mature miRNAs:	47
Transcripts:	ENST00000549830
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.

Markers in Region

D12S297

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	12	52,613,054 - 52,613,285	UniSTS	GRCh37
Build 36	12	50,899,321 - 50,899,552	RGD	NCBI36
Celera	12	51,415,495 - 51,415,731	RGD
Cytogenetic Map	12	q13.13	UniSTS
HuRef	12	49,646,332 - 49,646,567	UniSTS
Marshfield Genetic Map	12	64.96	UniSTS
Marshfield Genetic Map	12	64.96	RGD

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

Low

142

1313

387

493

227

696

Below cutoff

760

1215

834

208

391

1218

644

1397

177

514

999

136

537

866

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NR_027358	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC021066	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC039104	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BG211530	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068266	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000549830

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,930 - 52,223,804 (+)	Ensembl

RefSeq Acc Id:

ENST00000640420

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,164,115 - 52,223,800 (+)	Ensembl

RefSeq Acc Id:

ENST00000653127

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,899 - 52,223,749 (+)	Ensembl

RefSeq Acc Id:

ENST00000656394

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,920 - 52,223,809 (+)	Ensembl

RefSeq Acc Id:

ENST00000656951

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,930 - 52,223,749 (+)	Ensembl

RefSeq Acc Id:

ENST00000658977

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,899 - 52,223,752 (+)	Ensembl

RefSeq Acc Id:

ENST00000661213

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,221,339 - 52,223,749 (+)	Ensembl

RefSeq Acc Id:

ENST00000663735

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,909 - 52,223,813 (+)	Ensembl

RefSeq Acc Id:

ENST00000665995

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,935 - 52,223,813 (+)	Ensembl

RefSeq Acc Id:

ENST00000667021

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,930 - 52,223,749 (+)	Ensembl

RefSeq Acc Id:

ENST00000667981

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,890 - 52,223,749 (+)	Ensembl

RefSeq Acc Id:

ENST00000668114

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,920 - 52,223,748 (+)	Ensembl

RefSeq Acc Id:

ENST00000668621

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,941 - 52,223,749 (+)	Ensembl

RefSeq Acc Id:

ENST00000669247

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,911 - 52,223,813 (+)	Ensembl

RefSeq Acc Id:

ENST00000669936

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	52,210,911 - 52,223,749 (+)	Ensembl

RefSeq Acc Id:

NR_027358

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	12	52,210,930 - 52,223,880 (+)	NCBI
GRCh37	12	52,604,714 - 52,617,597 (+)	ENTREZGENE
HuRef	12	49,637,996 - 49,650,881 (+)	ENTREZGENE
CHM1_1	12	52,570,973 - 52,583,857 (+)	NCBI
T2T-CHM13v2.0	12	52,174,510 - 52,187,466 (+)	NCBI

Sequence:

show sequence

AGGCAGGTGGAGAGGGGATGGGGGAGGTCTCAGGTCCTCTTGCTCACCCATCAGCTGTGTAGTG
TCTGAAGTGATTAAGGAGCTTGGGGAGGCCTCCCAGGCTGGTCTGCTCCACTGGCCCTCAGAAA
GACTTGTCGCCTCGCCGAGCCTCAGTGTTCTCATCTGAAGAATAGAGTGGGCAAGGCCTTTCTC
CTACACACTCAGAGCCCTGAATGGGAAGAAATGGGTTCCATGTGCAGCAAGCCAGGAGAGATTT
AGGCAACGAGAACCTCCAGTTCTGTCTTAGGGTTCCCAGCTTTCTCCTTGTCCTGAGGGAGCCG
CTGAGCCTGTGGGAGATGAGGGGTGCCCATTCCCCAGTGCTTCTCACCCTCCCCCACCTGCCCT
CCTGGGGTACCTTTGTCTGCCACTTGCATCCTATTGGAAGCTGTCCCCAAGTGCGTGTTAGGCA
GGTGGCAGGTGCTGGAGCAGAGTGCACCACCCTCCGGCGATCACTGTGAGTTGGGGTAAGAGTG
GGGTGTTCCTGCCAGCCCCAGGAGAGGGGAAAGCAAGCCCCCGTCCACCCTTGTGGGTCTCTGC
TCCTGGAAAAGGTGCTCTAGCAGGCTCATCTGTGTGAGTCACTGTCTTCCATGTGGGGGGCTGT
GCTGAAGAAGCCTTGGTGATATGGGTGCAAATGCCAAAAACATGGAATGCTGGAAGCCAAGCTT
GCACATTCTAGGCAGCCATTTGGAAGATTCTTCTCTGCGCATGACCAGCTGAAAAGGAAAAACC
CCGAAACATTGGCACTGTGATTTCTCCATGTGAACAGTTTAGTTCGCCGAGGTGGACATGCCTC
ATTCATGCTTATGGAGTGACCGACCAGCCTTTAGTGACACCCCCTGAAATGTGAGTCATCCATG
GGTCACTAGTCATTGGAGAAGAGCCCCTTATACAAAACTTGGAGCTCAGACCACAAACAACAAC
AACAATCCAAAAAATAAAAAAATGAAAAATTAGGAGCAGAGACTAAATGGAAAGATGGAAATAT
TAAAATAAAAATATTATTTTAAAAATTAATATGTATTAAAATTTTATTTAAAGTAAAAATAAAT
AAAATAAAAAAATTAATATTAATTAATACCAAAAAAAAAAAAA

hide sequence

Promoters

RGD ID:

15096604

Promoter ID:

EPDNEWNC_H1442

Type:

initiation region

Name:

LINC00592_1

Description:

long intergenic non-protein coding RNA 592 [Source:HGNCSymbol;Acc:HGNC:27474]

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 Assembly	Chr	Position (strand)	Source
GRCh38	12	52,210,921 - 52,210,981	EPDNEWNC

Additional Information

External Database Links

Database	Acc Id	Source(s)
COSMIC	LINC00592	COSMIC
Ensembl Genes	ENSG00000258279	Ensembl, ENTREZGENE
Ensembl Transcript	ENST00000549830	ENTREZGENE
GTEx	ENSG00000258279	GTEx
HGNC ID	HGNC:27474	ENTREZGENE
Human Proteome Map	LINC00592	Human Proteome Map
NCBI Gene	LINC00592	ENTREZGENE
RNAcentral	URS0000ABD7CE	RNACentral

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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