LINC02175 (long intergenic non-protein coding RNA 2175)

Gene: LINC02175 (long intergenic non-protein coding RNA 2175) Homo sapiens

Analyze

Symbol:

LINC02175

Name:

long intergenic non-protein coding RNA 2175

RGD ID:

11667422

HGNC Page

HGNC:27550

Description:

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	16	25,066,887 - 25,068,955 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	16	25,066,937 - 25,088,618 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	16	25,078,208 - 25,080,276 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Cytogenetic Map	16	p12.1	NCBI
HuRef	16	23,171,748 - 23,173,644 (+)	NCBI		HuRef
CHM1_1	16	26,092,135 - 26,094,031 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	16	25,346,487 - 25,348,555 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

References

Additional References at PubMed

PMID:12477932	PMID:14702039

Genomics

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 16p13.11-12.1(chr16:14954894-28306843)x3	copy number gain	See cases [RCV000051828]	Chr16:14954894..28306843 [GRCh38] Chr16:15048751..28318164 [GRCh37] Chr16:14956252..28225665 [NCBI36] Chr16:16p13.11-12.1	pathogenic
GRCh38/hg38 16p12.2-11.2(chr16:21463739-29249579)x3	copy number gain	See cases [RCV000051829]	Chr16:21463739..29249579 [GRCh38] Chr16:21475060..29260900 [GRCh37] Chr16:21382561..29168401 [NCBI36] Chr16:16p12.2-11.2	pathogenic
GRCh38/hg38 16p12.2-11.2(chr16:21602183-29314373)x3	copy number gain	See cases [RCV000051842]	Chr16:21602183..29314373 [GRCh38] Chr16:21613504..29325694 [GRCh37] Chr16:21521005..29233195 [NCBI36] Chr16:16p12.2-11.2	pathogenic
GRCh38/hg38 16p13.3-11.2(chr16:4644892-29170820)x3	copy number gain	See cases [RCV000133809]	Chr16:4644892..29170820 [GRCh38] Chr16:4694893..29182141 [GRCh37] Chr16:4634894..29089642 [NCBI36] Chr16:16p13.3-11.2	pathogenic
GRCh38/hg38 16p12.2-11.2(chr16:22634385-29227323)x3	copy number gain	See cases [RCV000135594]	Chr16:22634385..29227323 [GRCh38] Chr16:22645706..29238644 [GRCh37] Chr16:22553207..29146145 [NCBI36] Chr16:16p12.2-11.2	likely pathogenic
GRCh38/hg38 16p12.2-11.2(chr16:21350622-29202837)x3	copy number gain	See cases [RCV000140235]	Chr16:21350622..29202837 [GRCh38] Chr16:21361943..29214158 [GRCh37] Chr16:21269444..29121659 [NCBI36] Chr16:16p12.2-11.2	likely pathogenic
GRCh38/hg38 16p12.2-11.2(chr16:23047969-30632245)x3	copy number gain	See cases [RCV000052401]	Chr16:23047969..30632245 [GRCh38] Chr16:23059290..30643566 [GRCh37] Chr16:22966791..30551067 [NCBI36] Chr16:16p12.2-11.2	pathogenic
GRCh38/hg38 16p12.2-12.1(chr16:21600992-28323344)x1	copy number loss	See cases [RCV000052519]	Chr16:21600992..28323344 [GRCh38] Chr16:21612313..28334665 [GRCh37] Chr16:21519814..28242166 [NCBI36] Chr16:16p12.2-12.1	pathogenic
GRCh38/hg38 16p12.2-11.2(chr16:23752047-31943755)x3	copy number gain	See cases [RCV000141141]	Chr16:23752047..31943755 [GRCh38] Chr16:23763368..31955076 [GRCh37] Chr16:23670869..31862577 [NCBI36] Chr16:16p12.2-11.2	pathogenic

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	271
Count of miRNA genes:	254
Interacting mature miRNAs:	270
Transcripts:	ENST00000571219
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

289

Low

1485

1572

1167

176

735

3229

1241

2618

200

907

1175

115

716

2105

Below cutoff

923

1304

501

395

1047

342

1111

941

1084

211

238

424

486

676

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NR_135196	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NR_135197	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC133552	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AI215529	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK093382	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AL834281	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC023651	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068262	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000571219

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,066,937 - 25,068,943 (+)	Ensembl

RefSeq Acc Id:

ENST00000653156

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,013 - 25,078,786 (+)	Ensembl

RefSeq Acc Id:

ENST00000654253

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,002 - 25,069,405 (+)	Ensembl

RefSeq Acc Id:

ENST00000654349

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,024 - 25,076,601 (+)	Ensembl

RefSeq Acc Id:

ENST00000655561

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,030 - 25,077,149 (+)	Ensembl

RefSeq Acc Id:

ENST00000657497

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,187 - 25,073,684 (+)	Ensembl

RefSeq Acc Id:

ENST00000657680

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,010 - 25,078,784 (+)	Ensembl

RefSeq Acc Id:

ENST00000657697

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,056 - 25,073,685 (+)	Ensembl

RefSeq Acc Id:

ENST00000658101

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,031 - 25,069,413 (+)	Ensembl

RefSeq Acc Id:

ENST00000658831

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,066,967 - 25,079,999 (+)	Ensembl

RefSeq Acc Id:

ENST00000660807

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,577 - 25,074,028 (+)	Ensembl

RefSeq Acc Id:

ENST00000665669

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,066 - 25,076,601 (+)	Ensembl

RefSeq Acc Id:

ENST00000666471

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,089 - 25,078,782 (+)	Ensembl

RefSeq Acc Id:

ENST00000667339

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,079 - 25,069,413 (+)	Ensembl

RefSeq Acc Id:

ENST00000668238

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,079 - 25,088,618 (+)	Ensembl

RefSeq Acc Id:

ENST00000670692

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	16	25,067,079 - 25,079,999 (+)	Ensembl

RefSeq Acc Id:

NR_135196

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	16	25,066,887 - 25,068,955 (+)	NCBI
CHM1_1	16	26,091,984 - 26,094,052 (+)	NCBI
T2T-CHM13v2.0	16	25,346,487 - 25,348,555 (+)	NCBI

Sequence:

show sequence

GGGCGGGGCCAACGGACCGCGGAGGCGGAGCCGCTACAGTCTGGGCGCTGGAGCGGTGGGAGCA
GCGCTCGTCCGCCGTTGGGGCCCCCAGCCCGCGCGCGTGAAGCAGCTAGCCGACCAAGCCCCGG
AAGGCGAGTGCCGGAGGGGGCGGGACAGCTCCTCCGGGGCCAGCGGGCACCAGGCTTGGGGGCT
GAGGCCCAGCGGCCCGAGACCAACTGGGCTGACCGAGGCCGCCTCCCCGCCAGCCCTGGGGTCC
ACTGCCCGGGGAGCAGCTCCCTTCCCAGGTCAGACTCGGGCTTCATCCTCTCTTGCCGCGCGCC
GAGCGGTTTTCAACTCTCACTGCTAGAATTCCTCCAACCACCCAGGATAGCAGGACCGAGATAC
ATGGCCACCCATGACCCGGAGCGTCCACTTCCAGGGACAGGCAGTGGTGATTGGCTTCGGTTGT
CATCTGTGCCATCTGTCCATGGTTCGAGAAGCTGCTGTTCACGTTTTGGGGAGGATCATGGTTT
GAGGGCTCCCGTGGTAGAATTTGGGGAGCTCTCATAGGCAGAAGGCTGAGAAAAGTTGGTGCTG
TGGGAAGTCAACTGGCAGCCGATGGAGTCGGGACCCGGGAGGAATGGAAAGGGAACCCAGATAG
GAAGCTACTGCAGTAGGCTCAGAGAGGTGATGACGGCAGGGCTAAGACAGCGGCCTTGGGCGGT
GACTGGGAAGAACGTTGAACACCGTGTTTGGGCTGAAGAAAAGAGCAAGGGAAGAGGTGAGGAA
CTTCAGTCCCAGCTGCTCTGGAGTTTGAGGCAGGAGGATGGCTTGAACCCAAGAGGTGGAGGCT
GAAGTGAGCCAAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGGGCAAAACCCTGTCTCTAA
AAAGAACTTTTTAAAAAAGCACCTGTAGATTTAAGCACATAATAACTACACTTTTGTCTGTTTT
ATTATGATATCAAAGTTAAATTTATGATGAATGACTAACTGGACAAAACTGAGAGCAACCACCA
CAGAGGTGAATATACTGAATGTATAACACTCTCTAATAATTTTAAGAACTCCGCTCTAATGAGC
AGATATCACAGAAAGAGACTTTTCAGATGAAATACCGATGACCAGGAAATCTGTGAGACCATTT
TAAAAAATTCGAAGTCATTGAAGAAATGCAAAGCTTCCAGGCTCCACTTTTCACTGATGAAATT
GGCAGAGTTTGGGACAATGAGATGTTGCTGTCCCGGGAGTGCGGATGGGGCTGTGTCCTGTGAT
GGCGGTGGGCACTGGCACTCTTGTCCAGAAAGACATTCACCACTGTGGTTCAAGAAGCACCTCA
AAGGTCTTCACCTTGGTCCCTTGTCCACCTCTGCCCGCGGTCTCTCCTCCTTTCAGCCTCCTCT
TTCCCACACAGTCCCTCCCGCCCTGGCTTGGTCCCCTTTCTTCTGACTGGGTCAGGCATGTGGG
TGACTCTTTGACTTCCAAGGCTCTGTCTACTTGGCTTTTTTCTTTCACCTGTTCTGCAGAATAA
CAGCCTGATTCGTTCCTCTTTTTGGGTCCTTCACTTCCATACCTGGGATTCGGGGCGTGGCCCA
GAAAGACCCTGCAGTCTTGCAGTGTGGGGCTGCCAGCATTTCATGGCCTCCAAGCTCAGCTGGG
CTGAATGAACGCTGCCATCCAGCGCTTGGCTCATTTTCTGTCCCATTTTCCTGAGTGCTTTTGC
CAGACTTACACTTTTCTGAAAGCTACTCCACCCTACCCCAGACACACCCTCTCTCCTCGGATGA
CCTGCCTCCTAATTTCCTGAGAAAACTGGACATGGCCACCTTTCCCCAGTGTCTGAGGCCCAGG
TTGACCCGTGGTCATGGTCGCTGTCACCACCCACCTGCCTGTATGACAGAGTGAGACCCTGTCT
CAAAAAAAAATAAAAAGAATGCCTCATGTTAAAAAAA

hide sequence

RefSeq Acc Id:

NR_135197

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	16	25,066,887 - 25,068,955 (+)	NCBI
CHM1_1	16	26,091,984 - 26,094,052 (+)	NCBI
T2T-CHM13v2.0	16	25,346,487 - 25,348,555 (+)	NCBI

Sequence:

show sequence

GGGCGGGGCCAACGGACCGCGGAGGCGGAGCCGCTACAGTCTGGGCGCTGGAGCGGTGGGAGCA
GCGCTCGTCCGCCGTTGGGGCCCCCAGCCCGCGCGCGTGAAGCAGCTAGCCGACCAAGCCCCGG
AAGGCGAGTGCCGGAGGGGGCGGGACAGCTCCTCCGGGGCCAGCGGGCACCAGGCTTGGGGGCT
GAGGCCCAGCGGCCCGAGACCAACTGGGCTGACCGAGGCCGCCTCCCCGCCAGCCCTGGGGTCC
ACTGCCCGGGGAGCAGCTCCCTTCCCAGGTCAGACTCGGGCTTCATCCTCTCTTGCCGCGCGCC
GAGCGGTTTTCAACTCTCACTGCTAGAATTCCTCCAACCACCCAGGATAGCAGGACCGAGATAC
ATGGCCACCCATGACCCGGAGCGTCCACTTCCAGGGACAGGCAGTGGTGATTGGCTTCGGTTGT
CATCTGTGCCATCTGTCCATGGTTCGAGAAGCTGCTGTTCACGTTTTGGGGAGGATCATGGTTT
GAGGGCTCCCGTGGTAGAATTTGGGGAGCTCTCATAGGCAGAAGGCTGAGAAAAGTTGGTGCTG
TGGGAAGTCAACTGGCAGCCGATGGAGTCGGGACCCGGGAGGAATGGAAAGGGAACCCAGATAG
GAAGCTACTGCAGTAGGCTCAGAGAGGTGATGACGGCAGGGCTAAGACAGCGGCCTTGGGCGGT
GACTGGGAAGAACGTTGAACACCGTGTTTGGGCTGAAGAAAAGAGCAAGGGAAGAGTCCCAGCT
GCTCTGGAGTTTGAGGCAGGAGGATGGCTTGAACCCAAGAGGTGGAGGCTGAAGTGAGCCAAGA
TCGCGCCACTGCACTCCAGCCTGGGCGACAGGGCAAAACCCTGTCTCTAAAAAGAACTTTTTAA
AAAAGCACCTGTAGATTTAAGCACATAATAACTACACTTTTGTCTGTTTTATTATGATATCAAA
GTTAAATTTATGATGAATGACTAACTGGACAAAACTGAGAGCAACCACCACAGAGGTGAATATA
CTGAATGTATAACACTCTCTAATAATTTTAAGAACTCCGCTCTAATGAGCAGATATCACAGAAA
GAGACTTTTCAGATGAAATACCGATGACCAGGAAATCTGTGAGACCATTTTAAAAAATTCGAAG
TCATTGAAGAAATGCAAAGCTTCCAGGCTCCACTTTTCACTGATGAAATTGGCAGAGTTTGGGA
CAATGAGATGTTGCTGTCCCGGGAGTGCGGATGGGGCTGTGTCCTGTGATGGCGGTGGGCACTG
GCACTCTTGTCCAGAAAGACATTCACCACTGTGGTTCAAGAAGCACCTCAAAGGTCTTCACCTT
GGTCCCTTGTCCACCTCTGCCCGCGGTCTCTCCTCCTTTCAGCCTCCTCTTTCCCACACAGTCC
CTCCCGCCCTGGCTTGGTCCCCTTTCTTCTGACTGGGTCAGGCATGTGGGTGACTCTTTGACTT
CCAAGGCTCTGTCTACTTGGCTTTTTTCTTTCACCTGTTCTGCAGAATAACAGCCTGATTCGTT
CCTCTTTTTGGGTCCTTCACTTCCATACCTGGGATTCGGGGCGTGGCCCAGAAAGACCCTGCAG
TCTTGCAGTGTGGGGCTGCCAGCATTTCATGGCCTCCAAGCTCAGCTGGGCTGAATGAACGCTG
CCATCCAGCGCTTGGCTCATTTTCTGTCCCATTTTCCTGAGTGCTTTTGCCAGACTTACACTTT
TCTGAAAGCTACTCCACCCTACCCCAGACACACCCTCTCTCCTCGGATGACCTGCCTCCTAATT
TCCTGAGAAAACTGGACATGGCCACCTTTCCCCAGTGTCTGAGGCCCAGGTTGACCCGTGGTCA
TGGTCGCTGTCACCACCCACCTGCCTGTATGACAGAGTGAGACCCTGTCTCAAAAAAAAATAAA
AAGAATGCCTCATGTTAAAAAAA

hide sequence

Promoters

RGD ID:

15096975

Promoter ID:

EPDNEWNC_H1812

Type:

initiation region

Name:

LINC02175_1

Description:

long intergenic non-protein coding RNA 2175 [Source:HGNCSymbol;Acc:HGNC:27550]

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	16	25,066,924 - 25,066,984	EPDNEWNC

Additional Information

External Database Links

Database	Acc Id	Source(s)
COSMIC	LINC02175	COSMIC
Ensembl Genes	ENSG00000262155	Ensembl, ENTREZGENE
Ensembl Transcript	ENST00000571219	ENTREZGENE
GTEx	ENSG00000262155	GTEx
HGNC ID	HGNC:27550	ENTREZGENE
Human Proteome Map	LINC02175	Human Proteome Map
NCBI Gene	LINC02175	ENTREZGENE
RNAcentral	URS0000A769BE	RNACentral
	URS0000A76A2C	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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