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Gene: LINC02245 (long intergenic non-protein coding RNA 2245) Homo sapiens

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Symbol:

LINC02245

Name:

long intergenic non-protein coding RNA 2245

RGD ID:

12790904

HGNC Page

HGNC:53134

Description:

ASSOCIATED WITH Spastic Tetraplegia, Thin Corpus Callosum, and Progressive Microcephaly; INTERACTS WITH aflatoxin B1; benzo[e]pyrene; methapyrilene

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	2	64,901,840 - 64,932,447 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	64,901,840 - 65,056,233 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	65,128,974 - 65,159,581 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	64,982,478 - 65,013,085 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	2	64,975,354 - 65,005,968 (-)	NCBI		Celera
Cytogenetic Map	2	p14	NCBI
HuRef	2	64,862,474 - 64,893,079 (-)	NCBI		HuRef
CHM1_1	2	65,059,977 - 65,090,581 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	2	64,911,457 - 64,942,061 (-)	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

spastic tetraplegia, thin corpus callosum, and progressive microcephaly (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

aflatoxin B1 (EXP)

benzo[e]pyrene (EXP)

methapyrilene (EXP)

silicon dioxide (EXP)

References

Additional References at PubMed

PMID:12477932	PMID:27827314	PMID:28839111	PMID:31999493

Genomics

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
NM_003038.5(SLC1A4):c.1120G>A (p.Gly374Arg)	single nucleotide variant	Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome [RCV003320284]	Chr2:65018156 [GRCh38] Chr2:65245290 [GRCh37] Chr2:2p14	likely pathogenic
GRCh38/hg38 2p16.1-11.2(chr2:58279519-83586962)x3	copy number gain	See cases [RCV000136053]	Chr2:58279519..83586962 [GRCh38] Chr2:58506654..83814086 [GRCh37] Chr2:58360158..83667597 [NCBI36] Chr2:2p16.1-11.2	pathogenic
GRCh38/hg38 2p14-13.3(chr2:64587095-69876311)x1	copy number loss	See cases [RCV000140691]	Chr2:64587095..69876311 [GRCh38] Chr2:64814229..70103443 [GRCh37] Chr2:64667733..69956947 [NCBI36] Chr2:2p14-13.3	likely pathogenic
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3	copy number gain	See cases [RCV000141494]	Chr2:7495123..87705899 [GRCh38] Chr2:7635254..88005418 [GRCh37] Chr2:7552705..87786533 [NCBI36] Chr2:2p25.1-11.2	benign
GRCh38/hg38 2p15-14(chr2:63311999-67309291)x1	copy number loss	See cases [RCV000054054]	Chr2:63311999..67309291 [GRCh38] Chr2:63539134..67536423 [GRCh37] Chr2:63392638..67389927 [NCBI36] Chr2:2p15-14	pathogenic

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	245
Count of miRNA genes:	234
Interacting mature miRNAs:	236
Transcripts:	ENST00000449259
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

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
376	1046	925	586	3504	607	1118	3	276	1709	143	1106	3378	2848	51	2791	383	1028	864	145

Sequence

Nucleotide Sequences


RefSeq Transcripts	NR_036586	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC007386	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC037562	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068276	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENST00000449259

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,901,840 - 64,905,137 (-)	Ensembl

Ensembl Acc Id:

ENST00000653778

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,902,305 - 65,056,168 (-)	Ensembl

Ensembl Acc Id:

ENST00000659575

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,945,590 - 64,952,048 (-)	Ensembl

Ensembl Acc Id:

ENST00000666526

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,047,504 - 65,056,227 (-)	Ensembl

Ensembl Acc Id:

ENST00000669631

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,953,253 - 65,048,179 (-)	Ensembl

Ensembl Acc Id:

ENST00000685506

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,047,511 - 65,056,207 (-)	Ensembl

Ensembl Acc Id:

ENST00000693405

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,904,114 - 64,932,449 (-)	Ensembl

Ensembl Acc Id:

ENST00000771808

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,920,776 - 65,056,228 (-)	Ensembl

Ensembl Acc Id:

ENST00000771809

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,953,063 - 65,048,212 (-)	Ensembl

Ensembl Acc Id:

ENST00000771810

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,945,634 - 64,989,915 (-)	Ensembl

Ensembl Acc Id:

ENST00000771811

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,020,242 - 65,056,168 (-)	Ensembl

Ensembl Acc Id:

ENST00000771812

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,904,114 - 64,932,444 (-)	Ensembl

Ensembl Acc Id:

ENST00000771813

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,030,487 - 65,056,209 (-)	Ensembl

Ensembl Acc Id:

ENST00000771814

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,030,487 - 65,056,205 (-)	Ensembl

Ensembl Acc Id:

ENST00000771815

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,030,487 - 65,056,174 (-)	Ensembl

Ensembl Acc Id:

ENST00000771816

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,030,483 - 65,056,168 (-)	Ensembl

Ensembl Acc Id:

ENST00000771817

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,030,580 - 65,056,168 (-)	Ensembl

Ensembl Acc Id:

ENST00000771818

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,030,716 - 65,056,205 (-)	Ensembl

Ensembl Acc Id:

ENST00000771819

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,970,277 - 64,990,267 (-)	Ensembl

Ensembl Acc Id:

ENST00000771820

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,030,493 - 65,049,339 (-)	Ensembl

Ensembl Acc Id:

ENST00000771821

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,917,694 - 64,932,414 (-)	Ensembl

Ensembl Acc Id:

ENST00000771822

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,970,277 - 64,982,416 (-)	Ensembl

Ensembl Acc Id:

ENST00000771823

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,047,515 - 65,056,233 (-)	Ensembl

Ensembl Acc Id:

ENST00000771824

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,047,888 - 65,056,174 (-)	Ensembl

Ensembl Acc Id:

ENST00000771825

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,047,892 - 65,056,174 (-)	Ensembl

Ensembl Acc Id:

ENST00000771826

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,946,037 - 64,950,403 (-)	Ensembl

Ensembl Acc Id:

ENST00000771827

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,979,783 - 64,982,462 (-)	Ensembl

Ensembl Acc Id:

ENST00000771828

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,920,779 - 64,922,645 (-)	Ensembl

Ensembl Acc Id:

ENST00000771829

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	64,921,156 - 64,922,619 (-)	Ensembl

Ensembl Acc Id:

ENST00000771830

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,030,487 - 65,031,712 (-)	Ensembl

Ensembl Acc Id:

ENST00000771831

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	65,047,892 - 65,048,215 (-)	Ensembl

RefSeq Acc Id:

NR_036586

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	2	64,901,840 - 64,932,447 (-)	NCBI
CHM1_1	2	65,059,977 - 65,090,581 (-)	NCBI
T2T-CHM13v2.0	2	64,911,457 - 64,942,061 (-)	NCBI

Sequence:

show sequence

GGTAACCTAGAGTTGAGAGATGGAGGAAGAGATACAGAATCTGGATGGCTATGCTCTGATCCTG
TAATCCGACTATGCCTGAATGTGGATCTACCTTCCAAAGGACTTCTCCAGCTCCATTTACAGTC
TGGCTCCTGGGCCTTTGGATCCCAGCAGTGTCCGAGCAGGAGCTCAAAGGACAGCCCCACCATG
GGGGATCAGCCCTAGAAGCTGTCACTACATCTCCAACGGACGCAACTATTTTCCAGGAACACCG
GGGGAGAGAGCCAACAACAGCACAGTGGCCCCGGACCGTGACCCTTGGACTGAAGGAACCTACA
GATGTGGTTTTTTTTGGTGACATTTTACATGCAACTCCAGATTTCAAACTCTTTTGGAGAAGCA
GGCAATCTGGCAACAGTCGTTTTGGATTCTCAGAAGGCAATAAAGAACAGCTGCCACCTTCCGA
GGGGCACGGTGGATGCCCTGTTCTGCCAGAATTGCCAACACGTTTATCGTCTTAGACTTGCCCA
AGGTGTCGCAGTTAGAGACTGCCTCCCTTATTCACGCTCCTGCCTGGTGCCCGTGGGCTTGAAT
TTGCTCCCCTTGGAGTGGGGTGAGGCTCTGCAGACACTTCTCATACACCTCCCCTGCAGACAGC
AAGCTCCTGGAACACAAGTCACATGCATTTCATTTCCTGCTCTCTTGCTACCACCCAACATGGG
CTCTCAATACATGTTGAAAGCAAGGATCAATGAATAAATGGGCAACTATCAGCTGTAGACTTGT
ATGTGCCAGGTATGGTGCTAGGCATGCTAGGCACCAAAAGGGCCACAGAGGTGTTACATGCCAG
GATATCAGGGAGTTCATGACATAGTGAGGGAAAGAAAAAGCTTATGCAGTGTGTGTGTGAAACT
TTAAGCAAACATGGTGCATAACAATAACAGGAATGACTTTGCCTGCCCCTGATGAAACTTCAGC
AGGGCTATGCCCTGTCTTGCCACCTTTAGGAAACAGCAGTCTTATAGTCCTTTGCCCCTCTGAG
TTACAACCACTGTCTCCTTTCAGGAGAATGCCCAGTGTTATATCATAATCAAGGCTTTGAACTT
GATGTGGCATTACATGTTCTTCCATCTCCCCAGCCACCTGAGAAGGGAGATGGGGTAGCTTTTC
TCTCTCACTCTCTCTCCCCCAACCCCTCCTTTTCCCACCGGCAGGTGAATGAGCTTCCTGCCCA
TAGGAGAAAGGGTAAAATCACAAGGTGGTGCCCTTGTCTCCAAATCTCAAGGTCCTCTGGATGG
CAGGTGAGTAAAGGTGACTCTTGTGATTATGGGTGTTTTGGGTGTTCCTCAGAGATCCCCCAAA
CTGGGGTCTTGTCCACCATTCCCAGGACTCTGCCATGTGGAGCCATGGGAATGTGAAGTTCACC
TCACACTTCCTTTCAGCTGAGGTCACCACACAGCCCCTACCAGCCCGGCTATATTGGGTGGGAT
TTCAGATGCCCCCACAATGGCTGCCTTGGAGACTTTCCACTGGTCCTCAAGAAGCAACAACGCT
CCCCTTGCTCTGCCTTTGGTGGAGGGCAATTCCTCCTCTCTCTCTGCCTGGCCCCAGGCTGCTT
CCACTGTCTCAGAAACTGGTCCCCGGATTCCCCCAGTTACAGAGAACCCTCATCAAGCTCTCAA
GTGGCCACTGAAACCCAGGCTCTCTAGGCTCTGGAGTATGGAAGTGACAGCTCCATTTAATTTC
TCCTTTCCTCTTGTAGGCTTACAGCATAGCACTCTCCCAAGAAATCATCCAAAAATTACCTCAA
CCATTCTATAGACCCCAAGCTGACCAGGGGAGGGAGGACCAAGAATCTTGAAACGTAAATACTA
CATTTGATGGTCTCCTTCAGACTTATTTTGGGATCTGATATCTCTTTAACAAAAATTATAAAAA
TTGAGGCAAAGAGAGCCCCATTTTTTATATACTGTTCTAATAAATAACAGGTACCCTTAGAAGA
ATGCAGACAAACACTCCTATGGAAATTTAAAGGAGCATAAGACTTCTTGCAGTATAGGGAGAGA
ACCAAGGAAGACTTCCTGGAGGAAATGGCCATTGAACTGGGCCTTGGACATGTGGAGGTGAGGG
ATGAGAGTATTCCAGATGAAGAGTCCAGCATAGGGAAGGCCCACAGGAAGGAATTGTGCTGTAT
TAATGCTGTCTTAGAGGCATTTCCATTGCCAGACACAGATACTCAAATTACTTCAGAGAGAGAG
AGAGAGAGTATTGAAAGGGTTTCTGTGAATACCTCCACAACTGTGGTTCTCAAAGTGTAATCCC
TGGGCCAGCAGCATCGGCATCACCTGGGAACTTGTTAGAAATGCAGATTCCCAGGCTGGGTGCA
GTGGCTCACGCCTGTAACCCTAGCACTTTGGGAGTCCGAGGTGGGTGGATCACCTGAGGTTGGG
AGTTTGAGACCAGCCTGACCAACATGGAGAAACCCTGTCTCTACTAAAAATACAAAAAGCCAGG
TGTGGTGGCGCATGCCTGTAATCCCAGCTGCTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACC
CGGGAGGCAGAGGTTGCGGTGAGCCGAGATTGCACCACTGCACTCCAGCCTGGGTAACAAGAGC
GAAACTCCACCGAAGAAAGAAGAGAGAGAGAGAGGGAGAAAGAAAGAAAGGAGAAAGAGAGAAA
GAAAGAAAAAGAAAGAAAGAAAAGAAAAGAAAAAAGAAAGGAAAAGAAAAGGCAAATTCACCAG
AGCCTTTGAATCAGAAAAGAACCCCCAGGGGCTGGTGGTAGCAGTCCTTGCACAGGCCCTCCAG
GTGATTCTCATCCAGGGAAGCCTGCGAGCCCTTGAGGTGGAATATTCTCAGGAATCCCTGAGAT
ATGTGAAGAACTGATGGCATAGGCTATTTCTAGGGAGGAAATGGGGCTGCTGGGTGCACAGATG
AGGGGAGGTGGGAGACCTCTGTAATTGTGTACCATGTGCATATATTACCTATTCAGAGAATAAT
AAAACAATGCGTTTAATCCCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Additional Information

External Database Links

Database	Acc Id	Source(s)
COSMIC	LINC02245	COSMIC
Ensembl Genes	ENSG00000237638	Ensembl
GTEx	ENSG00000237638	GTEx
HGNC ID	HGNC:53134	ENTREZGENE
Human Proteome Map	LINC02245	Human Proteome Map
NCBI Gene	LINC02245	ENTREZGENE
RNAcentral	URS000042883E	RNACentral
	URS000075C780	RNACentral
	URS0000EEB1C5	RNACentral
	URS0000EED34C	RNACentral
	URS0000EF502B	RNACentral
	URS00022B4CE8	RNACentral
	URS00022B56E9	RNACentral
	URS00025ECA2E	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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