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Gene: LINC02535 (long intergenic non-protein coding RNA 2535) Homo sapiens

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Symbol:

LINC02535

Name:

long intergenic non-protein coding RNA 2535

RGD ID:

12910366

HGNC Page

HGNC:53569

Description:

INTERACTS WITH aristolochic acid A; benzo[a]pyrene; O-methyleugenol

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	6	85,387,219 - 85,404,802 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	85,320,314 - 85,404,911 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	86,096,937 - 86,114,520 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Cytogenetic Map	6	q14.3	NCBI
HuRef	6	83,321,224 - 83,324,188 (-)	NCBI		HuRef
CHM1_1	6	86,194,881 - 86,197,843 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	6	86,604,337 - 86,621,920 (-)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
LINC02535	Human	aristolochic acid A	increases expression	EXP		6480464	aristolochic acid I results in increased expression of LINC02535 mRNA	CTD	PMID:33212167
LINC02535	Human	benzo[a]pyrene	decreases expression	EXP		6480464	Benzo(a)pyrene results in decreased expression of LINC02535 mRNA	CTD	PMID:32234424
LINC02535	Human	O-methyleugenol	decreases expression	EXP		6480464	methyleugenol results in decreased expression of LINC02535 mRNA	CTD	PMID:32234424
LINC02535	Human	okadaic acid	decreases expression	EXP		6480464	Okadaic Acid results in decreased expression of LINC02535 mRNA	CTD	PMID:38832940
LINC02535	Human	sodium arsenite	increases expression	EXP		6480464	sodium arsenite results in increased expression of LINC02535 mRNA	CTD	PMID:38568856

PMID:18487259	PMID:34125981	PMID:36577835

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 6q14.2-16.1(chr6:83838303-98822313)x1	copy number loss	See cases [RCV000135773]	Chr6:83838303..98822313 [GRCh38] Chr6:84548022..99270189 [GRCh37] Chr6:84604741..99376910 [NCBI36] Chr6:6q14.2-16.1	pathogenic
GRCh38/hg38 6q14.3-15(chr6:85370716-90669793)x1	copy number loss	See cases [RCV000136757]	Chr6:85370716..90669793 [GRCh38] Chr6:86080434..91379512 [GRCh37] Chr6:86137153..91436233 [NCBI36] Chr6:6q14.3-15	pathogenic
GRCh38/hg38 6q14.3-15(chr6:84926864-87365441)x1	copy number loss	See cases [RCV000137766]	Chr6:84926864..87365441 [GRCh38] Chr6:85636582..88075159 [GRCh37] Chr6:85693301..88131878 [NCBI36] Chr6:6q14.3-15	likely pathogenic
GRCh38/hg38 6q13-24.1(chr6:74382807-142040500)x3	copy number gain	See cases [RCV000139729]	Chr6:74382807..142040500 [GRCh38] Chr6:75092523..142361637 [GRCh37] Chr6:75149243..142403330 [NCBI36] Chr6:6q13-24.1	pathogenic
GRCh38/hg38 6q14.1-16.1(chr6:75926199-92710793)x1	copy number loss	See cases [RCV000143505]	Chr6:75926199..92710793 [GRCh38] Chr6:76635916..93420511 [GRCh37] Chr6:76692636..93477232 [NCBI36] Chr6:6q14.1-16.1	pathogenic
GRCh38/hg38 6q14.1-16.1(chr6:82569098-93753476)x1	copy number loss	See cases [RCV000052192]	Chr6:82569098..93753476 [GRCh38] Chr6:83278815..94463194 [GRCh37] Chr6:83335534..94519915 [NCBI36] Chr6:6q14.1-16.1	pathogenic

Predicted Target Of

	Summary Value
Count of predictions:	58
Count of miRNA genes:	58
Interacting mature miRNAs:	58
Transcripts:	ENST00000455071
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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
597496441	GWAS1592515_H	protein measurement QTL GWAS1592515 (human)		2e-110	protein measurement		6	85393838	85393839	Human
1298426	BFD3_H	Body fluid distribution QTL 3 (human)	2.79	0.01	Body fluid distribution	impedance ratio	6	84873647	110873647	Human

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

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
647	1615	1367	1297	3076	1207	1572	2	547	632	459	1046	3783	2987	33	2767	632	1293	964	102


RefSeq Transcripts	NR_134633	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NR_134634	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB371547	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK024998	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL135903	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068272	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENST00000455071

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	6	85,387,219 - 85,390,249 (-)	Ensembl

Ensembl Acc Id:

ENST00000840424

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	6	85,388,995 - 85,404,911 (-)	Ensembl

Ensembl Acc Id:

ENST00000840425

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	6	85,388,961 - 85,403,763 (-)	Ensembl

Ensembl Acc Id:

ENST00000840426

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	6	85,387,219 - 85,390,206 (-)	Ensembl

Ensembl Acc Id:

ENST00000840427

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	6	85,320,401 - 85,403,779 (-)	Ensembl

Ensembl Acc Id:

ENST00000840428

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	6	85,320,314 - 85,326,019 (-)	Ensembl

RefSeq Acc Id:

NR_134633

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	6	85,387,219 - 85,404,802 (-)	NCBI
CHM1_1	6	86,194,881 - 86,212,464 (-)	NCBI
T2T-CHM13v2.0	6	86,604,337 - 86,621,920 (-)	NCBI

Sequence:

show sequence

GATTCTTCCATCAAGGCTGGAACACAGGAGCAAATAGCTTGAACATACAAGGATTATATTGTTCCTTCTCTTAAAGTTACCTCTGTCATGCGCGTCCGTGTGAAGATACCACCAAACAGGCTTTGTAT
CTTCAGTTGCTTCAGGCCATCTGGATGTATACGTCAGGTCACAGGGGATATGATGGCTTAGCTTGGGCTCAGAGGCCTGACAACCTCCAGATTCAGAGTTCTTAACCTCTTTTTCCTGGAAGTTTGCT
GAGGAGCCAGATGCCTTGTGCTGACTTGTCTATTTTGAAAGAGGCTGCAGAAACACTCGATTCCACCTCAACCCGGAATTCAGCTTTCTTAGGAAAGGAAATAACCCCCGAAGCCTTTGCAACTAAGG
ACATGTATCCTTCAGACAAGTGTTTACTGGGCAACTTCTTCGTGCTGTAATTGAGTGTGGCCGATTGCTCACAAAGATGTTTGCAAAATCCCTCCTGTCCCCTAACTCACTTCTCCTTGCAGTGTCAC
TCTGCCAACTTCTCCTGTCGATTGGTGAAGACTGTTTCTCCTCCCCCTTGAATATGGGCTGGGCTTGTAACTTGCTTGACCAATAGAATGCAGAGAAATGAAATGCAGCCTTCAACATTCAAGGCTAT
GCTCAAGGAGTCTAACCCTGTGGATATGCTGTTGTCAAATGAGGGAGCTTCGATTAGCCTGTTGAAGACACACAGACGACCCGACAGGCAATACCAACATTCAGATATGCAAGTTATGCTGTCTTAGA
CCATGCTGCCCAGGTGAACTTTTAGACGACTGCAATTTGTGAGTGACTCTAGGCAAGACCAGAAGAAACTTCTAGCTAAATCTAAACCAAATGCCAACTCAGAATTGTAAGCAAATAAAACGGTTGTT
GTTTAAAGACACTAACTTTTGGGGTGTTTTGCCACACCTCAATACATAACTGTTACACTAATTATTTTTCATTGTGAAATCTTCAGCGTCTTATTCTGTAATCAAACCAGAATGTCCTTGCCTTCTTA
GCACTTTGCCACAGTCCAGTGGGGTGAATAGACAGCAGCTGCTCATTTATGCTCATGCTCATGTTCATAATTTGCATTTGGACTAAAAGGAGCTCTGTTCTCCAGGACAGAACTATTCTAAAGCTCTT
CAGGAACAGGAACAGGAGTCCATCACAGACAGCGAAATCAAAAGCGCCCTACATAGAGGCATCCAGACTGAGAGCTGAAAGGGATCTGGGAAATCATTTAGTCTCACTCCCTCATTTTCCATTCAGAC
CACAGGGATGAAAGAACTTGCTGAAGTTCTCACAGCTCTGTAGTGGCACAGTCAGAACAAGGATCCCAATCTCCTAACTACTAACATAAAATGCTTTCAGCATGCAAGTTGAGCATACAATGGGACAG
TTTAAATTTAAATGGTGTTTTGAGCAAGGGGAGAGTCTAATTAATTACTTCAAAGTATAATTTTGGAGTCACCAGAAAGGCGTTAAAGACAAAAAAATGCTTTGGAACCTAGGTGCTTCATATCTGAA
ATTGGGGCAGGTACAGGTGTATTCCTACCACTAAAGGGTCATTAGTTGGTTGGGTAGTCCTTTAGTGTTCTTGGTACTAAGCACAAAACATGGGTAAGATGGTTCAAGGCTGGTTGTGGTGGCTCATG
CCTATAGCCCCAGCATTTTAGGAGGCCAAGGCTGGAGGATAGCTTGAGCCCAGGAATTCGAGACAAGCCTGGGCAATATCGCAAGACCTTGTCTCTACAAATAATAATTTCTTAAGAATTGGCTGGGC
ATGGTGGCACACACCTGTAGGCTATTTGAGAGGTTGAGGTGGGAGGATTGCTTTAGTGTGGGAGGCTGAGGCTGCAATGAGGTGATCACACTATGGTACTACAGCCTGAGAAACAGTGTAAGATCCTG
CCTCAAAAAAAAAAAGTTTATGTTCTCAAAGTGCTCATAATCTAGTGGTAGTACAGTATTTGAGATATTAGAGCAGTTTCTCCTCCTTTTGCAACTAAGGACATGTATCTTTAAAGCAGAAGGAATGG
CAGAGTCGTGTAATAAACCCTCAAGTACCATTACTTAGCTTCAACAACTATCGACACTCTACTGTTCTTGTTTCATTTATGCCTCACCTCCTTCCCATCCCCCACTTGAATATTCTCATCCTTTTTTT
TTACAGTTTTTAAGATAACAATTACATAACTGAAATGCACAAATCTTAGCTGTACAGTTTTGACATATGGATACACCTGTGTAACCAATGACTGTATCACAACATAGAGCATTTCATCTCCCCAGCAA
GATCCATGTGTCTTTTCCTAGTTAATGCCTCTTTATTTCTGAGATGGTTATTGCTCTGCTTTTGTTTTTCATGTTAGGCTAGTCTTGCCTGTTCTAGAATTTCATATAACTGAGAACATACAGAATGT
ACTCACTAGTAGTGTCTGACTTTTTCACAAAGGATAATGTCTGTGGTATTCATTCATGCTGTTGTATGCATCAGTAGTTTATTTTCTTTTTACTATTAAGTAGTGTTCTAAGGACTATTTTAATAGCA
TCCCACAAAGGGGGTATGATATGTTCTATTTACATTATTATTTGGTTTGTAATATTTTATATTTTCTCTTGTGATTTCTCCTTTCACTCATGAATTATTATAATAAATTTTTTAAAGTGTATTATAAA
AAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

NR_134634

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	6	85,387,219 - 85,390,186 (-)	NCBI
CHM1_1	6	86,194,881 - 86,197,848 (-)	NCBI
T2T-CHM13v2.0	6	86,604,337 - 86,607,304 (-)	NCBI

Sequence:

show sequence

AGAAAAGAGGACAGAGTCATTTTGCTCAGAAGAAACAGCATGTGCAAATGTGCCACAACCATTC
AAAGCAAGTTGCTGCTTAAGTCTTGCCCACAACTTTTCATCTGAAAAGTGGAGTAGCTGAAGCAGCCAATGCTGGTGGTTATAATTCTTGAGGATGCAACAGTAAGAACGGAAAGGAAATAACCCCCG
AAGCCTTTGCAACTAAGGACATGTATCCTTCAGACAAGTGTTTACTGGGCAACTTCTTCGTGCTGTAATTGAGTGTGGCCGATTGCTCACAAAGATGTTTGCAAAATCCCTCCTGTCCCCTAACTCAC
TTCTCCTTGCAGTGTCACTCTGCCAACTTCTCCTGTCGATTGGTGAAGACTGTTTCTCCTCCCCCTTGAATATGGGCTGGGCTTGTAACTTGCTTGACCAATAGAATGCAGAGAAATGAAATGCAGCC
TTCAACATTCAAGGCTATGCTCAAGGAGTCTAACCCTGTGGATATGCTGTTGTCAAATGAGGGAGCTTCGATTAGCCTGTTGAAGACACACAGACGACCCGACAGGCAATACCAACATTCAGATATGC
AAGTTATGCTGTCTTAGACCATGCTGCCCAGGTGAACTTTTAGACGACTGCAATTTGTGAGTGACTCTAGGCAAGACCAGAAGAAACTTCTAGCTAAATCTAAACCAAATGCCAACTCAGAATTGTAA
GCAAATAAAACGGTTGTTGTTTAAAGACACTAACTTTTGGGGTGTTTTGCCACACCTCAATACATAACTGTTACACTAATTATTTTTCATTGTGAAATCTTCAGCGTCTTATTCTGTAATCAAACCAG
AATGTCCTTGCCTTCTTAGCACTTTGCCACAGTCCAGTGGGGTGAATAGACAGCAGCTGCTCATTTATGCTCATGCTCATGTTCATAATTTGCATTTGGACTAAAAGGAGCTCTGTTCTCCAGGACAG
AACTATTCTAAAGCTCTTCAGGAACAGGAACAGGAGTCCATCACAGACAGCGAAATCAAAAGCGCCCTACATAGAGGCATCCAGACTGAGAGCTGAAAGGGATCTGGGAAATCATTTAGTCTCACTCC
CTCATTTTCCATTCAGACCACAGGGATGAAAGAACTTGCTGAAGTTCTCACAGCTCTGTAGTGGCACAGTCAGAACAAGGATCCCAATCTCCTAACTACTAACATAAAATGCTTTCAGCATGCAAGTT
GAGCATACAATGGGACAGTTTAAATTTAAATGGTGTTTTGAGCAAGGGGAGAGTCTAATTAATTACTTCAAAGTATAATTTTGGAGTCACCAGAAAGGCGTTAAAGACAAAAAAATGCTTTGGAACCT
AGGTGCTTCATATCTGAAATTGGGGCAGGTACAGGTGTATTCCTACCACTAAAGGGTCATTAGTTGGTTGGGTAGTCCTTTAGTGTTCTTGGTACTAAGCACAAAACATGGGTAAGATGGTTCAAGGC
TGGTTGTGGTGGCTCATGCCTATAGCCCCAGCATTTTAGGAGGCCAAGGCTGGAGGATAGCTTGAGCCCAGGAATTCGAGACAAGCCTGGGCAATATCGCAAGACCTTGTCTCTACAAATAATAATTT
CTTAAGAATTGGCTGGGCATGGTGGCACACACCTGTAGGCTATTTGAGAGGTTGAGGTGGGAGGATTGCTTTAGTGTGGGAGGCTGAGGCTGCAATGAGGTGATCACACTATGGTACTACAGCCTGAG
AAACAGTGTAAGATCCTGCCTCAAAAAAAAAAAGTTTATGTTCTCAAAGTGCTCATAATCTAGTGGTAGTACAGTATTTGAGATATTAGAGCAGTTTCTCCTCCTTTTGCAACTAAGGACATGTATCT
TTAAAGCAGAAGGAATGGCAGAGTCGTGTAATAAACCCTCAAGTACCATTACTTAGCTTCAACAACTATCGACACTCTACTGTTCTTGTTTCATTTATGCCTCACCTCCTTCCCATCCCCCACTTGAA
TATTCTCATCCTTTTTTTTTACAGTTTTTAAGATAACAATTACATAACTGAAATGCACAAATCTTAGCTGTACAGTTTTGACATATGGATACACCTGTGTAACCAATGACTGTATCACAACATAGAGC
ATTTCATCTCCCCAGCAAGATCCATGTGTCTTTTCCTAGTTAATGCCTCTTTATTTCTGAGATGGTTATTGCTCTGCTTTTGTTTTTCATGTTAGGCTAGTCTTGCCTGTTCTAGAATTTCATATAAC
TGAGAACATACAGAATGTACTCACTAGTAGTGTCTGACTTTTTCACAAAGGATAATGTCTGTGGTATTCATTCATGCTGTTGTATGCATCAGTAGTTTATTTTCTTTTTACTATTAAGTAGTGTTCTA
AGGACTATTTTAATAGCATCCCACAAAGGGGGTATGATATGTTCTATTTACATTATTATTTGGTTTGTAATATTTTATATTTTCTCTTGTGATTTCTCCTTTCACTCATGAATTATTATAATAAATTT
TTTAAAGTGTATTATAAAAAAAAAAAAAAAAAA

hide sequence

RGD ID:

15096038

Promoter ID:

EPDNEWNC_H881

Type:

initiation region

Name:

LINC02535_1

Description:

long intergenic non-protein coding RNA 2535 [Source:HGNCSymbol;Acc:HGNC:53569]

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	6	85,390,208 - 85,390,268	EPDNEWNC

Database	Acc Id	Source(s)
COSMIC	LINC02535	COSMIC
Ensembl Genes	ENSG00000234155	Ensembl, ENTREZGENE
Ensembl Transcript	ENST00000455071	ENTREZGENE
GTEx	ENSG00000234155	GTEx
HGNC ID	HGNC:53569	ENTREZGENE
Human Proteome Map	LINC02535	Human Proteome Map
NCBI Gene	LINC02535	ENTREZGENE
RNAcentral	URS0000621C9B	RNACentral
	URS0000A76479	RNACentral
	URS0000A766D0	RNACentral

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


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


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