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Gene: LINC00342 (long intergenic non-protein coding RNA 342) Homo sapiens

Analyze

Symbol:

LINC00342

Name:

long intergenic non-protein coding RNA 342

RGD ID:

5488137

HGNC Page

HGNC:42470

Description:

Biomarker of Huntington's disease.

Type:

ncrna (Ensembl: lncRNA)

RefSeq Status:

VALIDATED

Previously known as:

NCRNA00342

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	2	95,807,052 - 95,826,981 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	95,806,973 - 95,835,003 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	96,472,800 - 96,492,729 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Cytogenetic Map	2	q11.1	NCBI
HuRef	2	90,440,085 - 90,460,016 (-)	NCBI		HuRef
CHM1_1	2	96,477,195 - 96,497,126 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	2	96,504,222 - 96,524,153 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Huntington's disease (IEP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

acrylamide (EXP)

aristolochic acid A (EXP)

beta-lapachone (EXP)

bisphenol A (EXP)

butanal (EXP)

cadmium dichloride (EXP)

dorsomorphin (EXP)

methylisothiazolinone (EXP)

methylmercury chloride (EXP)

SB 431542 (EXP)

sodium arsenite (EXP)

thimerosal (EXP)

toluene (EXP)

trichostatin A (EXP)

valproic acid (EXP)

Molecular Pathway Annotations Click to see Annotation Detail View

Huntington's disease pathway (IEP)

References

References - curated

#	Reference Title	Reference Citation
1.	Long non-coding RNAs in Huntington's disease neurodegeneration.	Johnson R Neurobiol Dis. 2012 May;46(2):245-54. doi: 10.1016/j.nbd.2011.12.006. Epub 2011 Dec 14.
2.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:14702039	PMID:29507755	PMID:30320899	PMID:31469292	PMID:31539128	PMID:32213297	PMID:34715819	PMID:35168108	PMID:35452205	PMID:36878503	PMID:37933652

Genomics

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 2q11.1-11.2(chr2:95493468-96977610)x3	copy number gain	See cases [RCV000133839]	Chr2:95493468..96977610 [GRCh38] Chr2:96159216..97643347 [GRCh37] Chr2:95522943..97007074 [NCBI36] Chr2:2q11.1-11.2	uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95674981-96052275)x3	copy number gain	See cases [RCV000135080]	Chr2:95674981..96052275 [GRCh38] Chr2:96340729..96718023 [GRCh37] Chr2:95704456..96081750 [NCBI36] Chr2:2q11.1-11.2	benign
GRCh38/hg38 2q11.1-11.2(chr2:95337458-99072953)x3	copy number gain	See cases [RCV000138012]	Chr2:95337458..99072953 [GRCh38] Chr2:96003206..99689416 [GRCh37] Chr2:95366933..99055848 [NCBI36] Chr2:2q11.1-11.2	uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95766541-97589743)x3	copy number gain	See cases [RCV000137817]	Chr2:95766541..97589743 [GRCh38] Chr2:96432289..98206206 [GRCh37] Chr2:95796016..97572638 [NCBI36] Chr2:2q11.1-11.2	uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95809285-96006224)x3	copy number gain	See cases [RCV000141062]	Chr2:95809285..96006224 [GRCh38] Chr2:96475033..96671972 [GRCh37] Chr2:95838760..96035699 [NCBI36] Chr2:2q11.1-11.2	benign
GRCh38/hg38 2q11.1-13(chr2:94678532-110602409)x3	copy number gain	See cases [RCV000141075]	Chr2:94678532..110602409 [GRCh38] Chr2:95344257..111359986 [GRCh37] Chr2:94707984..111076455 [NCBI36] Chr2:2q11.1-13	pathogenic
GRCh38/hg38 2p11.2-q11.2(chr2:91443218-102334856)x3	copy number gain	See cases [RCV000052945]	Chr2:91443218..102334856 [GRCh38] Chr2:91617683..102951316 [GRCh37] Chr2:90981410..102317748 [NCBI36] Chr2:2p11.2-q11.2	pathogenic
GRCh38/hg38 2q11.1-12.1(chr2:94817406-103252396)x3	copy number gain	See cases [RCV000052946]	Chr2:94817406..103252396 [GRCh38] Chr2:95618109..103868854 [GRCh37] Chr2:94846878..103235286 [NCBI36] Chr2:2q11.1-12.1	pathogenic
GRCh38/hg38 2q11.1-11.2(chr2:95806265-97285797)x3	copy number gain	See cases [RCV000053136]	Chr2:95806265..97285797 [GRCh38] Chr2:96472013..98013866 [GRCh37] Chr2:95835740..97380005 [NCBI36] Chr2:2q11.1-11.2	uncertain significance
GRCh38/hg38 2q11.1-11.2(chr2:95810453-97024341)x3	copy number gain	See cases [RCV000053137]	Chr2:95810453..97024341 [GRCh38] Chr2:96476201..97690078 [GRCh37] Chr2:95839928..97053805 [NCBI36] Chr2:2q11.1-11.2	uncertain significance

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	121
Count of miRNA genes:	58
Interacting mature miRNAs:	58
Transcripts:	ENST00000412393, ENST00000448494
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.

QTLs in Region (GRCh38)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
407274304	GWAS923280_H	migraine disorder, diastolic blood pressure QTL GWAS923280 (human)		5e-34	migraine disorder, diastolic blood pressure	diastolic blood pressure (CMO:0000005)	2	95825708	95825709	Human

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

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
1204	2432	2788	2245	4940	1721	2342	4	620	1948	462	2266	7279	6454	52	3708	847	1731	1611	170

Sequence

Nucleotide Sequences


RefSeq Transcripts	NR_103734	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC008268	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK057592	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK057596	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK093195	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL832439	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC117383	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC126153	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068276	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENST00000412393

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,118 - 95,814,776 (-)	Ensembl

Ensembl Acc Id:

ENST00000448494

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,118 - 95,816,215 (-)	Ensembl

Ensembl Acc Id:

ENST00000655069

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,055 - 95,814,326 (-)	Ensembl

Ensembl Acc Id:

ENST00000657232

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,061 - 95,817,831 (-)	Ensembl

Ensembl Acc Id:

ENST00000659287

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,118 - 95,814,993 (-)	Ensembl

Ensembl Acc Id:

ENST00000660416

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,062 - 95,819,724 (-)	Ensembl

Ensembl Acc Id:

ENST00000660608

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,806,973 - 95,815,817 (-)	Ensembl

Ensembl Acc Id:

ENST00000660641

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,052 - 95,815,156 (-)	Ensembl

Ensembl Acc Id:

ENST00000661329

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,828,204 - 95,835,003 (-)	Ensembl

Ensembl Acc Id:

ENST00000662121

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,118 - 95,833,963 (-)	Ensembl

Ensembl Acc Id:

ENST00000663557

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,070 - 95,818,459 (-)	Ensembl

Ensembl Acc Id:

ENST00000664191

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,055 - 95,815,790 (-)	Ensembl

Ensembl Acc Id:

ENST00000668171

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,054 - 95,814,307 (-)	Ensembl

Ensembl Acc Id:

ENST00000824807

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,062 - 95,814,793 (-)	Ensembl

Ensembl Acc Id:

ENST00000824808

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,807,062 - 95,814,791 (-)	Ensembl

Ensembl Acc Id:

ENST00000824809

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	95,813,379 - 95,817,835 (-)	Ensembl

RefSeq Acc Id:

NR_103734

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	2	95,807,052 - 95,826,981 (-)	NCBI
HuRef	2	90,440,085 - 90,460,016 (-)	NCBI
CHM1_1	2	96,477,195 - 96,497,126 (-)	NCBI
T2T-CHM13v2.0	2	96,504,222 - 96,524,153 (+)	NCBI

Sequence:

show sequence

GGGGCAAGATAGCCAACTAGAAGCAGCTGCAATTCGAGGCTCCCACTGAGAAGAACTAAAACAG
TGTGCAAATCCTGCACCAGCAACTGACATATCCAGGTTCTATGATCAGGACTGACTAGGTAGTT
GGCATGGCCCATAGAGAACAAGGAAAGATGGGCTGGTGGATTGGCCCACCTGGGAGCCACATGG
GGCAAGGGGAGCCCTCACCCTCAGCCAGCCAAGGGAGGCAGTGAGTGAGCATGCTACCCAGCCT
GGGAAACTGCTTTTTCCATGGATCTTTGCAATCCACAGATCAGAAGATCCCACTCATGAGACCA
CACCACCAGGGCCTTGGGTGCCAACTACAGAGCCATGCAGATTCTCAACAGCCACTCAGCTGGA
GTCTGCCTAAAAAGTTGGGGAGGGTTGTCATCATCACTGTGGCTGCCTGCTGCCTAAACCCTCT
GAGTTCCCTGGGGGAGGGGGAGCAGTCATCACTGTGGTTGCTGGCTGCCTAAGACAACTGAGCT
TCCCAAGAGAGGGGCAGTCATCATCACTGCAGCTGCCTGCTGCCTGAGGAAACTGAGCTCCCCA
AGAAGGGACAGCAGCCATCACTGTGGCTGCTAGCTGCCTAAGACACTGAACTCCTGGGGAGGAA
GGGCGGCAGCCATTTCTACAGAGCCAGGCTGCTGTTTTTCCTTTGCTGATGCCAGGGAGACTGG
ACGGCTTGGTCCCAAGAGGTATTCCCCACAGCGCAGCATACTGGCTGTGGCAGATCATGGCCAG
ACTGCCTCTTTAGGCTGACCCTCACCCATCCCTCCTCACTGGGTGGGGCATCCCTGCAGGAACT
CCAGCAACTCAAGCCAGGGAATTAGGGAGAGAACTCTGATCTCTCTAAGTCTGAGTCCCTAGCA
GGAGGGGTGGCTGGCTGTTGTCTCCACAAACCAGAAGACTTATTCTTTCCCCCTGCTCACTCTG
AGGAATCCAGGCATCCCAGACGAGTGGGATTTCCCCCAGCACAGCATACCCCCTTCACAAAGGG
ACAACTAAAGTGCTTCATTAAGCAAGTCCTGGATCCTGTGCCCCCCAACTGGGTGAGACACCCC
AATGGGTCACCAGACACCTTATACAAGAGCATTTCTACTGGCATCAGGTGGGTGCCCCTCAAGG
ACAGAGATCCCAGAGGAAGGAGTGGGGTCTCATCTTTGCTGTTCTCCAGCACTCTCTGGTGACA
TCTTCAGGTGTGGGAGGGACCCAGATAAGTAGGGCTTGAAGTGAATCCCCAGCAAACTGCAGCA
GCCCTACAGAAGAGGTGCCTGACTGTTCAAAGGAAAACAGAAAGCAACAACAACATCAACCAAA
AAGTCCCCACGAAAACCTCATCTAAAGGTCAGCAGCCTCAAAGATCAAAATGAGACAAACTCAT
GAAGATGAGAAAGGAATGAAAAACCCCTCACAACTCAAAAGGCCAGAGTGGCTTGTTTACTCCA
AATGATCACAACACCTCTACAGCAAGGGCACAGTGCTGGGAGGAGGTTGAGATGGATGAATTGA
CAGAAGTAGGCTTCAGAAGGTGGGTAGTAGCAAACTTCACTGAGCTAAAGGAGCACGTTCTAAC
CCAACACATTGGAACGAATCCCAGAACTTAAAGATTGGTTCTCTAAAATAAGACAGACAAAAAT
AAAAAAGAATAAAACGGAAGGAACAAAACCTCCAATAAGTATGGGGTTATGTATAGAGGCCAAT
TCTACAAATCACTGGCATCCCTGAAAGGGAGGTGGAGAAATCAATGCATTGGGTTAGAACATGC
TCCTTTAGCTCTGTGAAATTTGTTATTACCCACCTTCTGAACCCTACTTCTGTCAGCAAAGAAG
CTAAGAACCATGTTAAAAGGTTACAGAAGATGCTAACTAGAATAACCAGTTTAGAGAGGAACAT
AAATGACCGGAGCCAACTATAAAGCACATAAGGGGAACTTCGTGATGCAAACACAAGTATCAAC
AGCTGAATTGATCAAGCAGAAAAAAGAATATCAGAGCTTGAAGACTATCTTGCCAAAATAAGGC
AGGCAGACAAGATTAGAGAAAAAAGAATGAAAAGGAATGAACAAAACCTCAAAGAACTGTGGAA
CTATGTAAAAGACCAAACCTATGACTGCTTGGACTACCTGAAAGAGACAAGGAGAATGGAGCCA
CGTTGGGAAAACACACTTCAAGATATCATCCAGGAGAACTTCCCCAACCTAGCAAGACAGGCCA
ACATTCAAATTCAGGAAATCCAGAGAACCCCAGTAAGATACTCCACAAGAAAATCAACCCTCAA
GACACATAGTCATCAGATTCTCCAAGATCAAAATGAAGGAAAAAATGTTAAAGGCAGCCAGAGA
CAAGGGCAGGTCACCTACAAGGGGAAGCCCGTCAGACTAACCGTGGGCCTCTCAGCAGAAACCC
TACAAGCCAGAAGACAGTTGGGTCCAATGGTCAACATTCTTAGAGAAAAGAATTTCTAACCTAG
AATTTCATATCTGGCCAAACTAACCTTCATAAGTGAAGGAGAAATCCTTCTCAGACAAGCAAAT
GCTGAGGGAATTTATCACCACCAGGCCTGCCTTGCAAGACCTCCTGAAGGAAGCACTAAAGATG
GAAAGGAATCAGAATGATGCTGGCCTCATAAAATGAGTTAGGGAGGATTTCCTCTTTTTCTATT
GATTGGAATAGTTTCAGAAGGAATGGTACCAGTTCCTCCTTGTACCTCTGGTAGAATTCGGCTG
TGAATCCATCTGGTCCTGGACTCTTTTTGTTTCTCCACAGACACTACCCAAAGCAGTCCTTCAC
TACAGTGGCAGACAGACCTGAAAATTTTCATCTGAAGCAGCAGAGTGAACTGCAGAGTCAGAGA
TAGAATCTCACTATGTTGACCAGGCTGGTCTTGAACTCTTGGCACCCAAGCGATCCTTTTGCCT
GGAATCCCAAAGTGTCAGATTTACTGAAGAATATTTCATTGTAATTACTTTTTATACTTTATAG
GTCAAGAGCTCTGTTTTAAAGACAAAATTTATTGAATATACTTTTTCAAACAAAGTTTCATGTT
CTAATCATTGTCTGATTTCAGCATTAAATGAAACACAGTAAAGAAAGTTGGGCTGA

hide sequence

Promoters

RGD ID:

15095462

Promoter ID:

EPDNEWNC_H286

Type:

initiation region

Name:

LINC00342_1

Description:

long intergenic non-protein coding RNA 342 [Source:HGNCSymbol;Acc:HGNC:42470]

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	2	95,814,762 - 95,814,822	EPDNEWNC

Additional Information

External Database Links

Database	Acc Id	Source(s)
COSMIC	LINC00342	COSMIC
Ensembl Genes	ENSG00000232931	Ensembl
GTEx	ENSG00000232931	GTEx
HGNC ID	HGNC:42470	ENTREZGENE
Human Proteome Map	LINC00342	Human Proteome Map
NCBI Gene	150759	ENTREZGENE
RNAcentral	URS000075C528	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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