LINC00620 (long intergenic non-protein coding RNA 620)

Gene: LINC00620 (long intergenic non-protein coding RNA 620) Homo sapiens

Analyze

Symbol:

LINC00620

Name:

long intergenic non-protein coding RNA 620

RGD ID:

6771241

HGNC Page

HGNC:44223

Description:

ASSOCIATED WITH 3p deletion syndrome; INTERACTS WITH aflatoxin B1; benzo[a]pyrene; bisphenol A

Type:

ncrna (Ensembl: lncRNA)

RefSeq Status:

VALIDATED

Previously known as:

AC093611.1

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	3	13,650,721 - 13,746,635 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	3	13,650,696 - 13,746,638 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	3	13,692,221 - 13,788,132 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Celera	3	13,630,484 - 13,726,447 (+)	NCBI		Celera
Cytogenetic Map	3	p25.1	NCBI
HuRef	3	13,625,687 - 13,721,788 (+)	NCBI		HuRef
CHM1_1	3	13,642,235 - 13,738,149 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	3	13,651,199 - 13,747,267 (+)	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

3p deletion syndrome (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

aflatoxin B1 (EXP)

benzo[a]pyrene (EXP)

bisphenol A (EXP)

fulvestrant (EXP)

leflunomide (EXP)

permethrin (EXP)

References

Additional References at PubMed

PMID:21368711	PMID:23092984	PMID:23478628

Genomics

Variants

Variants in LINC00620
7 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 3p25.1(chr3:13325295-13882924)x4	copy number gain	See cases [RCV000137624]	Chr3:13325295..13882924 [GRCh38] Chr3:13366795..13924421 [GRCh37] Chr3:13341795..13899422 [NCBI36] Chr3:3p25.1	uncertain significance
GRCh38/hg38 3p26.3-24.1(chr3:32241-30064208)x3	copy number gain	See cases [RCV000138004]	Chr3:32241..30064208 [GRCh38] Chr3:73914..30105699 [GRCh37] Chr3:48914..30080703 [NCBI36] Chr3:3p26.3-24.1	pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:32241-20334387)x3	copy number gain	See cases [RCV000137941]	Chr3:32241..20334387 [GRCh38] Chr3:73914..20375879 [GRCh37] Chr3:48914..20350883 [NCBI36] Chr3:3p26.3-24.3	pathogenic
GRCh38/hg38 3p26.3-22.1(chr3:53308-41381521)x3	copy number gain	See cases [RCV000141810]	Chr3:53308..41381521 [GRCh38] Chr3:94991..41423012 [GRCh37] Chr3:69991..41398016 [NCBI36] Chr3:3p26.3-22.1	pathogenic
GRCh38/hg38 3p26.1-25.1(chr3:7356110-14360442)x3	copy number gain	See cases [RCV000143766]	Chr3:7356110..14360442 [GRCh38] Chr3:7397797..14401942 [GRCh37] Chr3:7372797..14376946 [NCBI36] Chr3:3p26.1-25.1	pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:52066-20280127)x3	copy number gain	See cases [RCV000051690]	Chr3:52066..20280127 [GRCh38] Chr3:93749..20321619 [GRCh37] Chr3:68749..20296623 [NCBI36] Chr3:3p26.3-24.3	pathogenic
GRCh38/hg38 3p26.3-24.1(chr3:52266-29248782)x3	copy number gain	Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]\|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051718]\|See cases [RCV000051718]	Chr3:52266..29248782 [GRCh38] Chr3:93949..29290273 [GRCh37] Chr3:68949..29265277 [NCBI36] Chr3:3p26.3-24.1	pathogenic
GRCh38/hg38 3p26.3-24.3(chr3:63843-19510600)x3	copy number gain	See cases [RCV000051719]	Chr3:63843..19510600 [GRCh38] Chr3:105526..19552092 [GRCh37] Chr3:80526..19527096 [NCBI36] Chr3:3p26.3-24.3	pathogenic
GRCh38/hg38 3p25.3-22.2(chr3:11463328-38919543)x3	copy number gain	See cases [RCV000051720]	Chr3:11463328..38919543 [GRCh38] Chr3:11504802..38961034 [GRCh37] Chr3:11479802..38936038 [NCBI36] Chr3:3p25.3-22.2	pathogenic
GRCh38/hg38 3p26.3-22.2(chr3:52266-37148076)x3	copy number gain	See cases [RCV000051097]	Chr3:52266..37148076 [GRCh38] Chr3:93949..37189567 [GRCh37] Chr3:68949..37164571 [NCBI36] Chr3:3p26.3-22.2	pathogenic
Single allele	deletion	3p- syndrome [RCV002280352]	Chr3:13371737..20095506 [GRCh38] Chr3:3p25.1-24.3	pathogenic

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	410
Count of miRNA genes:	212
Interacting mature miRNAs:	217
Transcripts:	ENST00000419618, ENST00000438915
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.

Markers in Region

D3S3608

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	3	13,704,250 - 13,704,419	UniSTS	GRCh37
Build 36	3	13,679,251 - 13,679,420	RGD	NCBI36
Celera	3	13,642,513 - 13,642,684	RGD
Cytogenetic Map	3	p25.1	UniSTS
HuRef	3	13,637,716 - 13,637,887	UniSTS
Marshfield Genetic Map	3	38.28	RGD
Marshfield Genetic Map	3	38.28	UniSTS
Genethon Genetic Map	3	33.5	UniSTS
TNG Radiation Hybrid Map	3	8266.0	UniSTS
deCODE Assembly Map	3	32.42	UniSTS

D3S100

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	3	13,733,579 - 13,733,794	UniSTS	GRCh37
Build 36	3	13,708,580 - 13,708,795	RGD	NCBI36
Celera	3	13,671,848 - 13,672,063	RGD
Cytogenetic Map	3	p25.1	UniSTS
HuRef	3	13,667,144 - 13,667,359	UniSTS

WI-10346

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	3	13,698,241 - 13,698,514	UniSTS	GRCh37
Build 36	3	13,673,242 - 13,673,515	RGD	NCBI36
Celera	3	13,636,504 - 13,636,777	RGD
Cytogenetic Map	3	p25.1	UniSTS
HuRef	3	13,631,707 - 13,631,980	UniSTS
Whitehead-RH Map	3	62.3	UniSTS

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

Low

333

422

Below cutoff

230

261

258

292

598

208

2267

213

296

165

291

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NR_027103	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC090509	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC093611	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC039529	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068275	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KF457598	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KF573664	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KF573665	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KF573669	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KF573709	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000419618

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	3	13,650,721 - 13,746,637 (+)	Ensembl

RefSeq Acc Id:

ENST00000438915

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	3	13,650,696 - 13,746,629 (+)	Ensembl

RefSeq Acc Id:

ENST00000665476

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	3	13,650,733 - 13,746,638 (+)	Ensembl

RefSeq Acc Id:

NR_027103

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	3	13,650,721 - 13,746,635 (+)	NCBI
GRCh37	3	13,692,221 - 13,788,132 (+)	NCBI
HuRef	3	13,625,687 - 13,721,788 (+)	NCBI
CHM1_1	3	13,642,235 - 13,738,149 (+)	NCBI
T2T-CHM13v2.0	3	13,651,199 - 13,747,267 (+)	NCBI

Sequence:

show sequence

CCGGTGCGGGCCGGTGCGGGCCAGTGCAGGCCAGGCCCGGCCGGGGCGAGGCAGGTGGCCAGGT
CCGAGGACCGCGTCGCACAGCAGCTTTCAGGACCTGGAGAGAAATCGAGATGAAGAAGGGAAGT
CACTTGCTTCATGGCCAGGGAAGGGCTCCAGCAAGACATGGGCTCCTGAAAGTGACAGTGTGTG
AAGGCCCGGAGAGGCACAGGACCTGTCCCCTCGCCCTCCTTGGATTGCAGCAAGGAAAGAGGTG
TGTCTTCCGCAGAAAAATGTGCATGTTCTTTTAGATGTGTGGCCTCCGAGCAAGGTATTTAGCC
TGCCTCTATGTGCTCACCTGGAAAATGGGGTGATGAAGAAGATGATGATGATAATGGGAACTCC
CTCTTGGAGCTGCTGTGCAGATGAATTTTCCTTCTAACAGTCAGGCCCCTCTGCTGCAAGTCTG
CTGGAGTTTTCTGGAGGTCCACTCCAGACCTTGTTTGCCTGGGTATCACCAGCCGAGGCTGCAG
AACAGCAAAGATTGCTGCCTGTTCCTTCCTTTGGAAGCTTTGTCCCAGGGAGGCACCCACCAGA
TGCCAGCTGGAGCTCTTCTGTATAAGGAAAAGTGGGCAAGTTTTGAGTTCAACGTGAGGCCTCA
AGGATGTGTGCAACCCATGGTACTTGAATTTACTTATTGACTGTTTTTTGGAAATCCTTATTTC
CCAAAACTCGTGGAAGGAGCTGACTTCTGGCAGGAAACGTGGAACTGGCAGCGTGTCGTGCAAG
CATCTGCAATCCCAGTCCTGAGCTGGACTTCTCAGAGAGGCTGGGCATTATTTATGGAGATGTC
GGAGTGACAGGGGGAACTTCTGGCCAGGAACTGCCGGTGGTGTCACATCCTTAACCTGGCTGAC
ATCGGAACACCCTGGGGGGAGCATTTCTCCAGGAAAGGATGGTGGGTCAGGAGCCCGCATGGTG
TCTTTTCAAAGCAATAATAAAGATATCAGAAGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Promoters

RGD ID:

15095570

Promoter ID:

EPDNEWNC_H409

Type:

initiation region

Name:

LINC00620_1

Description:

long intergenic non-protein coding RNA 620 [Source:HGNCSymbol;Acc:HGNC:44223]

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	3	13,650,743 - 13,650,803	EPDNEWNC

Additional Information

External Database Links

Database	Acc Id	Source(s)
COSMIC	LINC00620	COSMIC
Ensembl Genes	ENSG00000224514	Ensembl, ENTREZGENE
Ensembl Transcript	ENST00000419618	ENTREZGENE
GTEx	ENSG00000224514	GTEx
HGNC ID	HGNC:44223	ENTREZGENE
Human Proteome Map	LINC00620	Human Proteome Map
NCBI Gene	LINC00620	ENTREZGENE
RNAcentral	URS000075D5C0	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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