LINC00408 (long intergenic non-protein coding RNA 408)

Gene: LINC00408 (long intergenic non-protein coding RNA 408) Homo sapiens

Analyze

Symbol:

LINC00408

Name:

long intergenic non-protein coding RNA 408

RGD ID:

7248624

HGNC Page

HGNC:42740

Description:

Type:

ncrna (Ensembl: lncRNA)

RefSeq Status:

VALIDATED

Previously known as:

RP11-442J17.2

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	13	18,905,439 - 18,926,741 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	13	18,905,419 - 18,935,554 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	13	19,479,579 - 19,500,881 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Cytogenetic Map	13	q12.11	NCBI
HuRef	13	284,943 - 305,698 (+)	NCBI		HuRef
CHM1_1	13	19,453,571 - 19,474,862 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	13	18,099,875 - 18,121,174 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

References

References - curated

#	Reference Title	Reference Citation
1.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations

Additional References at PubMed

PMID:12477932

Genomics

Variants

Variants in LINC00408
1 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
NR_104118.1(LINC00408):n.649+6694C>A	single nucleotide variant	Lung cancer [RCV000097764]	Chr13:18915760 [GRCh38] Chr13:19489900 [GRCh37] Chr13:13q12.11	uncertain significance
GRCh38/hg38 13q11-34(chr13:18445862-114327173)x1	copy number loss	See cases [RCV000135610]	Chr13:18445862..114327173 [GRCh38] Chr13:19020001..115085141 [GRCh37] Chr13:10098739..114110750 [NCBI36] Chr13:13q11-34	pathogenic
GRCh38/hg38 13q11-34(chr13:18456040-114340285)x3	copy number gain	See cases [RCV000140004]	Chr13:18456040..114340285 [GRCh38] Chr13:19030180..115105760 [GRCh37] Chr13:17928180..114123862 [NCBI36] Chr13:13q11-34	pathogenic
GRCh38/hg38 13q11-13.2(chr13:18862146-33577351)x3	copy number gain	See cases [RCV000141867]	Chr13:18862146..33577351 [GRCh38] Chr13:19436286..34151488 [GRCh37] Chr13:18334286..33049488 [NCBI36] Chr13:13q11-13.2	pathogenic
GRCh38/hg38 13q11-12.11(chr13:18862146-22489174)x3	copy number gain	See cases [RCV000142006]	Chr13:18862146..22489174 [GRCh38] Chr13:19436286..23063313 [GRCh37] Chr13:18334286..21961313 [NCBI36] Chr13:13q11-12.11	pathogenic
GRCh38/hg38 13q11-34(chr13:18862146-114342258)x3	copy number gain	See cases [RCV000143462]	Chr13:18862146..114342258 [GRCh38] Chr13:19436286..115107733 [GRCh37] Chr13:18334286..114125835 [NCBI36] Chr13:13q11-34	pathogenic
GRCh38/hg38 13q11-34(chr13:18565048-114327173)x3	copy number gain	See cases [RCV000053719]	Chr13:18565048..114327173 [GRCh38] Chr13:19139188..115085141 [GRCh37] Chr13:18037188..114110750 [NCBI36] Chr13:13q11-34	pathogenic
GRCh38/hg38 13q11-13.3(chr13:18676442-37656039)x3	copy number gain	See cases [RCV000053721]	Chr13:18676442..37656039 [GRCh38] Chr13:19250582..38230176 [GRCh37] Chr13:18148582..37128176 [NCBI36] Chr13:13q11-13.3	pathogenic
GRCh38/hg38 13q11-34(chr13:18850545-114327173)x3	copy number gain	See cases [RCV000053723]	Chr13:18850545..114327173 [GRCh38] Chr13:19296527..115085141 [GRCh37] Chr13:18194527..114110750 [NCBI36] Chr13:13q11-34	pathogenic

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	62
Count of miRNA genes:	62
Interacting mature miRNAs:	62
Transcripts:	ENST00000447784
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.

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			1		2			2	1		121	3
Low	16		5		14		46	5	6	3	256	21
Below cutoff	60	37	42	24	46	19	123	30	66	15	39	61	7	14	43	1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NR_104118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC245087	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC245149	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL355516	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC035261	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068265	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000447784

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,439 - 18,907,810 (+)	Ensembl

RefSeq Acc Id:

ENST00000653982

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,419 - 18,908,443 (+)	Ensembl

RefSeq Acc Id:

ENST00000660513

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,431 - 18,926,738 (+)	Ensembl

RefSeq Acc Id:

ENST00000663325

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,429 - 18,926,665 (+)	Ensembl

RefSeq Acc Id:

ENST00000663501

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,450 - 18,926,740 (+)	Ensembl

RefSeq Acc Id:

ENST00000663692

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,446 - 18,926,738 (+)	Ensembl

RefSeq Acc Id:

ENST00000664751

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,444 - 18,926,740 (+)	Ensembl

RefSeq Acc Id:

ENST00000665951

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,466 - 18,926,738 (+)	Ensembl

RefSeq Acc Id:

ENST00000668892

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,430 - 18,926,743 (+)	Ensembl

RefSeq Acc Id:

ENST00000669381

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,464 - 18,935,554 (+)	Ensembl

RefSeq Acc Id:

ENST00000671023

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	13	18,905,430 - 18,926,738 (+)	Ensembl

RefSeq Acc Id:

NR_104118

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	13	18,905,439 - 18,926,741 (+)	NCBI
HuRef	13	284,943 - 305,698 (+)	NCBI
CHM1_1	13	19,453,571 - 19,474,862 (+)	NCBI
T2T-CHM13v2.0	13	18,099,875 - 18,121,174 (+)	NCBI

Sequence:

show sequence

GCTTAGAGAACAGGAAGTGGGAGCCACATACCCCGAGCTGGCGGCTTGAGCCTGTGGTATCTAG
GCTCACCTCACTGCGGTTGGTGGAGGTGATGGAGGTTGCAGCTTGGCCAGCATGGTAGAAAGGT
GGCAGGGTAGACTCTAGATTCTAGAGGGCAACCTCTGTTTGCTCATGCTGGAGCGTGGCAGGTG
CACAATGTTTCCTTGGGAATCCTCAGCAGGGCACGTCTGGCTTTTACCACCCAGTTGCTTCGAG
CCAGGAGATGGAGGAGTCATCTGTTGCACGCTGGAGGCTGGAGCCTGCAGATGGCATGGTTCTG
TGGCTCACCTCGCTGCAGTTGGTGGCAGAGACAGAGACTGCAGCTTGACCAGAGTGGTGGAGTG
AGTATTGTCATCTGCATGAGCAAATCTGGTTCATCACATCTTTGCAACAGGAAAAGGAAGGGAG
GATCATGTGTATAATGTTTTAAGGCCAAGATTCACAACAAGAACAAAGTCTTTATTAACTTTTG
CCTTCAAGAACCTGCAGTGTTGAGCCCTTTTTTATTTCTGGTTGGAGTGCAGTGGCATGATCTT
GACTCACTGCAACCTCCACCTCCCGGGTTCAAGCCATTCTCTTCCCTCAGCCTCCTCAGTAGCT
GGATTACAGATATGTATCTCAAGAGCACTCCACAACAAAGATTCTGCCTGCAATCCTCCACTTC
AAGGTCTGTTCCAGGAAACCTGTGTAACACAGTTATGCATAGAGTGGTCTTAGGAAGCTGACTC
TAACATGAAAATTTAGAGTTGGATCTTTTGCTGACATATTGAATATTCATAAGAGCATATGATA
CATTTGTCTATCATAAACATGTCATTTCAAAAAACCCTCAAAGTTGCCTTGTAGAACATAATTT
TAAAACTAGTGTGTAGGAATATTTCATATCAGTTATTCAGTCTTCTTAATATCTGAACCGAAAT
TAATCTTCCATTCTGCTTTTATTTATAAATAATGATTTATTGTCAGATTCAATAATTTATATTT
TCATTTATTCTAAGGTAGGAAATACCAGCATAAAAATAAATTATTTGAAACAAATCA

hide sequence

Promoters

RGD ID:

15096715

Promoter ID:

EPDNEWNC_H1525

Type:

initiation region

Name:

LINC00408_1

Description:

long intergenic non-protein coding RNA 408 [Source:HGNCSymbol;Acc:HGNC:42740]

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	13	18,905,465 - 18,905,525	EPDNEWNC

Additional Information

External Database Links

Database	Acc Id	Source(s)
COSMIC	LINC00408	COSMIC
Ensembl Genes	ENSG00000226250	Ensembl, ENTREZGENE
Ensembl Transcript	ENST00000663692	ENTREZGENE
GTEx	ENSG00000226250	GTEx
HGNC ID	HGNC:42740	ENTREZGENE
Human Proteome Map	LINC00408	Human Proteome Map
NCBI Gene	LINC00408	ENTREZGENE
RNAcentral	URS000075BD4F	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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