LINC01411 (long intergenic non-protein coding RNA 1411)

Gene: LINC01411 (long intergenic non-protein coding RNA 1411) Homo sapiens

Analyze

Symbol:

LINC01411

Name:

long intergenic non-protein coding RNA 1411

RGD ID:

9068849

HGNC Page

HGNC:50703

Description:

INTERACTS WITH aflatoxin B1; benzo[a]pyrene; benzo[e]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	5	174,336,354 - 174,527,139 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	5	174,336,295 - 174,532,457 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	5	173,763,357 - 173,954,142 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Cytogenetic Map	5	q35.2	NCBI
HuRef	5	169,049,566 - 169,050,488 (+)	NCBI		HuRef
CHM1_1	5	173,385,789 - 173,386,711 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	5	174,877,309 - 175,068,065 (+)	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)

benzo[a]pyrene (EXP)

benzo[e]pyrene (EXP)

methapyrilene (EXP)

O-methyleugenol (EXP)

References

Additional References at PubMed

PMID:16344560	PMID:25422238

Genomics

Variants

Variants in LINC01411
7 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 5q33.3-35.3(chr5:156825512-181269805)x3	copy number gain	See cases [RCV000133847]	Chr5:156825512..181269805 [GRCh38] Chr5:156252523..180696806 [GRCh37] Chr5:156185101..180629412 [NCBI36] Chr5:5q33.3-35.3	pathogenic
GRCh38/hg38 5q35.2(chr5:173949773-174900395)x1	copy number loss	See cases [RCV000135638]	Chr5:173949773..174900395 [GRCh38] Chr5:173376776..174327398 [GRCh37] Chr5:173309382..174260004 [NCBI36] Chr5:5q35.2	pathogenic
GRCh38/hg38 5q34-35.3(chr5:164386701-181269805)x3	copy number gain	See cases [RCV000135546]	Chr5:164386701..181269805 [GRCh38] Chr5:163813707..180696806 [GRCh37] Chr5:163746285..180629412 [NCBI36] Chr5:5q34-35.3	pathogenic
GRCh38/hg38 5q35.2(chr5:174116318-174632800)x3	copy number gain	See cases [RCV000139637]	Chr5:174116318..174632800 [GRCh38] Chr5:173543321..174059803 [GRCh37] Chr5:173475927..173992409 [NCBI36] Chr5:5q35.2	likely benign\|uncertain significance
GRCh38/hg38 5q35.1-35.3(chr5:169334755-181285301)x3	copy number gain	See cases [RCV000141249]	Chr5:169334755..181285301 [GRCh38] Chr5:168761759..180712302 [GRCh37] Chr5:168694337..180644908 [NCBI36] Chr5:5q35.1-35.3	pathogenic
GRCh38/hg38 5q35.1-35.2(chr5:173237772-176614618)x3	copy number gain	See cases [RCV000142647]	Chr5:173237772..176614618 [GRCh38] Chr5:172664775..176041619 [GRCh37] Chr5:172597381..175974225 [NCBI36] Chr5:5q35.1-35.2	pathogenic
GRCh38/hg38 5q32-35.3(chr5:149714592-181272151)x3	copy number gain	See cases [RCV000051863]	Chr5:149714592..181272151 [GRCh38] Chr5:149094155..180699152 [GRCh37] Chr5:149074348..180631758 [NCBI36] Chr5:5q32-35.3	pathogenic
GRCh38/hg38 5q33.3-35.3(chr5:160029980-181269805)x3	copy number gain	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051865]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051865]\|See cases [RCV000051865]	Chr5:160029980..181269805 [GRCh38] Chr5:159456987..180696806 [GRCh37] Chr5:159389565..180629412 [NCBI36] Chr5:5q33.3-35.3	pathogenic
GRCh38/hg38 5q34-35.3(chr5:168689326-181269946)x3	copy number gain	See cases [RCV000051866]	Chr5:168689326..181269946 [GRCh38] Chr5:168116331..180696947 [GRCh37] Chr5:168048909..180629553 [NCBI36] Chr5:5q34-35.3	pathogenic
GRCh38/hg38 5q35.1-35.2(chr5:172961091-175054665)x1	copy number loss	See cases [RCV000052150]	Chr5:172961091..175054665 [GRCh38] Chr5:172388094..174481668 [GRCh37] Chr5:172320700..174414274 [NCBI36] Chr5:5q35.1-35.2	pathogenic
NR_125806.1(LINC01411):n.223+6268A>G	single nucleotide variant	Lung cancer [RCV000095582]	Chr5:174342844 [GRCh38] Chr5:173769847 [GRCh37] Chr5:5q35.2	uncertain significance
GRCh38/hg38 5q35.1-35.2(chr5:172776798-174342969)x1	copy number loss	See cases [RCV000052149]	Chr5:172776798..174342969 [GRCh38] Chr5:172203801..173769972 [GRCh37] Chr5:172136407..173702578 [NCBI36] Chr5:5q35.1-35.2	pathogenic

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	1236
Count of miRNA genes:	707
Interacting mature miRNAs:	811
Transcripts:	ENST00000504512, ENST00000506862, ENST00000507361, ENST00000510234, ENST00000511707, ENST00000515513
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	14	18	4	3		3		5	43	4	7	10	1
Low	60	628	45	2	18	3	79	25	2632	26	157	46	2	1	29
Below cutoff	1331	1221	473	171	547	66	3110	996	821	92	813	426	113	441	2130	3

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NR_125806	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC008381	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC025752	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC108104	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC108112	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BG330133	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BM051440	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BU620825	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BX110485	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068273	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	DA346958	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000504512

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	5	174,503,683 - 174,526,380 (+)	Ensembl

RefSeq Acc Id:

ENST00000506862

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	5	174,517,759 - 174,532,457 (+)	Ensembl

RefSeq Acc Id:

ENST00000507361

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	5	174,336,354 - 174,529,982 (+)	Ensembl

RefSeq Acc Id:

ENST00000510234

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	5	174,336,495 - 174,527,139 (+)	Ensembl

RefSeq Acc Id:

ENST00000511707

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	5	174,503,815 - 174,520,665 (+)	Ensembl

RefSeq Acc Id:

ENST00000515513

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	5	174,336,295 - 174,526,448 (+)	Ensembl

RefSeq Acc Id:

ENST00000664184

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	5	174,523,864 - 174,528,764 (+)	Ensembl

RefSeq Acc Id:

ENST00000685618

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	5	174,503,683 - 174,504,758 (+)	Ensembl

RefSeq Acc Id:

ENST00000687783

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	5	174,503,695 - 174,504,758 (+)	Ensembl

RefSeq Acc Id:

NR_125806

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	5	174,336,354 - 174,527,139 (+)	NCBI
CHM1_1	5	173,196,210 - 173,386,711 (+)	NCBI
T2T-CHM13v2.0	5	174,877,309 - 175,068,065 (+)	NCBI

Sequence:

show sequence

CCTTCCCCAGCTTTGGGGCCACAGAGGGACAGAAACCGCAGGCAGGCTGGCCTGGGAATGAACC
TACACCAGCCTGAAGTCAGAAGAGCCTCTAGGAGCCTCCAGCCTGGACTCTTTTTACAGATGGG
GAAACTGAGTCCCAGAGAGGGAGCAATGAAGGATGTCTAAGGTCATCAGCAACGTAAAGCCAAC
AGCATCATCCTGAGTCATGTTTGAACCTGAGGGAAAGAAACATATGTTCGAAGAGGTTCTGAGG
CTGCTGCACCCGATATCATACCTGGTTGGCCCTGGGAAAGGGCCCACCTCCAATACATAAACAC
AACCAGCTTTGACAGTGAGCCCTGAAGCATGGCATTGAGAAGCTGCCTAAGAAGGAGGCAGATC
CATCAGCCTGGGTGCCCGACTGATTACCCTGAGCAGAGCTCCCCAGCCCACCTGTGATGGACGC
ATGGAGCTTGAGCAAGGAATAAATATTCGTTGCTGGACTCTGATTACACTGGACCTATCCAAGA
TCTGAGATCATCAACTCATCTCAAAATCCTTAAGCTGACCACAGCAGCATCGTCCCTTTTGCAG
TGTAAGGGAGCCCAGCTGGGACAATGTGTGAATCAACGCATGAAGGAGTGAGTGAGCAGCTAAC
CAAATGAAAGAATACTCAGATATCTGGGGTACAGTTCCCCTCCAGGTTTGCACAGCATCTGCTG
AAGTCTCCACTAGAAACTCAATGGAAGGTCCCCACCGGAAACTGAAAGTCTCCTAGAGTGGCTT
TGAGTTGCGGTTTCACCCTCCCTGCAGATCCACAGGGGAGGCTGGGGCAGATGGAAAATACCAA
CTTGATGGTCTGTGGCCACACCATGCTGCTCCCCAAGGCCCCTCAGAATTTCACTGCCCAATAT
GGTAGCGCCCAGCCTGAAACGTGGCCAGTGTGAATTGAGATGGGCTGGAAATGCACCAGACTTC
CAAGAGCTGGACAAAAACCATATACGTAAAGTATCTTTGTTTTACATATTTGTACTGATGACAC
AATGAAATCATATTTAGGGTATTTTCTGTTACATAAAATACATTACTAAAATTAAAAAAAAAAA
AAAAAAA

hide sequence

Promoters

RGD ID:

15095979

Promoter ID:

EPDNEWNC_H819

Type:

initiation region

Name:

LINC01411_2

Description:

long intergenic non-protein coding RNA 1411 [Source:HGNCSymbol;Acc:HGNC:50703]

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	5	174,336,262 - 174,336,322	EPDNEWNC

RGD ID:

15095980

Promoter ID:

EPDNEWNC_H820

Type:

initiation region

Name:

LINC01411_1

Description:

long intergenic non-protein coding RNA 1411 [Source:HGNCSymbol;Acc:HGNC:50703]

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	5	174,503,683 - 174,503,743	EPDNEWNC

Additional Information

External Database Links

Database	Acc Id	Source(s)
COSMIC	LINC01411	COSMIC
Ensembl Genes	ENSG00000249306	Ensembl, ENTREZGENE
Ensembl Transcript	ENST00000510234	ENTREZGENE
GTEx	ENSG00000249306	GTEx
HGNC ID	HGNC:50703	ENTREZGENE
Human Proteome Map	LINC01411	Human Proteome Map
NCBI Gene	LINC01411	ENTREZGENE
RNAcentral	URS00007E506F	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)

Send us a Message