LINC00362 (long intergenic non-protein coding RNA 362) - Rat Genome Database

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Gene: LINC00362 (long intergenic non-protein coding RNA 362) Homo sapiens
Analyze
Symbol: LINC00362
Name: long intergenic non-protein coding RNA 362
RGD ID: 6481234
HGNC Page HGNC:42682
Description: ASSOCIATED WITH autosomal recessive limb-girdle muscular dystrophy type 2C; paraplegia; Schizophrenia
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: MODEL
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381323,169,829 - 23,170,872 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1323,169,835 - 23,170,597 (-)EnsemblGRCh38hg38GRCh38
Cytogenetic Map13q12.12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

Genomics

Variants

.
Variants in LINC00362
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 13q12.12(chr13:22992823-23499449)x1 copy number loss See cases [RCV000053282] Chr13:22992823..23499449 [GRCh38]
Chr13:23566962..24073588 [GRCh37]
Chr13:22464962..22971588 [NCBI36]
Chr13:13q12.12		 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 13q12.12(chr13:22764286-24444616)x3 copy number gain See cases [RCV000135612] Chr13:22764286..24444616 [GRCh38]
Chr13:23338425..25018754 [GRCh37]
Chr13:22236425..23916754 [NCBI36]
Chr13:13q12.12		 likely benign
NC_000013.11:g.22924987_24337204del deletion See cases [RCV003313804] Chr13:22924987..24337204 [GRCh38]
Chr13:13q12.12		 uncertain significance
NC_000013.11:g.(?_23093196)_(23203899_?)del deletion Autosomal recessive limb-girdle muscular dystrophy type 2C [RCV000798820] Chr13:23093196..23203899 [GRCh38]
Chr13:23667335..23778038 [GRCh37]
Chr13:13q12.12		 pathogenic
GRCh38/hg38 13q12.11-34(chr13:18946182-114304628)x3 copy number gain See cases [RCV000053726] Chr13:18946182..114304628 [GRCh38]
Chr13:19520322..115070103 [GRCh37]
Chr13:18418322..114088205 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q12.11-12.3(chr13:18958091-31090460)x3 copy number gain See cases [RCV000053729] Chr13:18958091..31090460 [GRCh38]
Chr13:19532231..31664597 [GRCh37]
Chr13:18430231..30562597 [NCBI36]
Chr13:13q12.11-12.3		 pathogenic
GRCh38/hg38 13q12.11-34(chr13:19837395-114327173)x3 copy number gain See cases [RCV000053731] Chr13:19837395..114327173 [GRCh38]
Chr13:20411535..115085141 [GRCh37]
Chr13:19309535..114110750 [NCBI36]
Chr13:13q12.11-34		 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 13q12.11-14.11(chr13:19671934-40914767)x3 copy number gain See cases [RCV000137892] Chr13:19671934..40914767 [GRCh38]
Chr13:20246074..41488903 [GRCh37]
Chr13:19144074..40386903 [NCBI36]
Chr13:13q12.11-14.11		 pathogenic
GRCh38/hg38 13q12.12(chr13:22943845-24355293)x3 copy number gain See cases [RCV000138877] Chr13:22943845..24355293 [GRCh38]
Chr13:23517984..24929431 [GRCh37]
Chr13:22415984..23827431 [NCBI36]
Chr13:13q12.12		 uncertain significance|conflicting data from submitters
GRCh38/hg38 13q12.12(chr13:22980365-24370481)x3 copy number gain See cases [RCV000138208] Chr13:22980365..24370481 [GRCh38]
Chr13:23554504..24944619 [GRCh37]
Chr13:22452504..23842619 [NCBI36]
Chr13:13q12.12		 uncertain significance
GRCh38/hg38 13q12.12(chr13:23106962-23856032)x1 copy number loss See cases [RCV000133647] Chr13:23106962..23856032 [GRCh38]
Chr13:23681101..24430171 [GRCh37]
Chr13:22579101..23328171 [NCBI36]
Chr13:13q12.12		 pathogenic
GRCh38/hg38 13q12.12(chr13:22992823-24336605)x3 copy number gain See cases [RCV000051234] Chr13:22992823..24336605 [GRCh38]
Chr13:23566962..24910743 [GRCh37]
Chr13:22464962..23808743 [NCBI36]
Chr13:13q12.12		 uncertain significance
GRCh38/hg38 13q12.12(chr13:22941375-24286142)x3 copy number gain See cases [RCV000051307] Chr13:22941375..24286142 [GRCh38]
Chr13:23515514..24860280 [GRCh37]
Chr13:22413514..23758280 [NCBI36]
Chr13:13q12.12		 uncertain significance
NC_000013.11:g.(?_22968338)_(24323208_?)del deletion Schizophrenia [RCV000754142] Chr13:22968338..24323208 [GRCh38]
Chr13:13q12.12		 likely pathogenic
GRCh38/hg38 13q12.11-34(chr13:19833130-114327106)x3 copy number gain See cases [RCV000139078] Chr13:19833130..114327106 [GRCh38]
Chr13:20407270..115085141 [GRCh37]
Chr13:19305270..114110683 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q12.12(chr13:23045243-24253602)x1 copy number loss See cases [RCV000134882] Chr13:23045243..24253602 [GRCh38]
Chr13:23619382..24827740 [GRCh37]
Chr13:22517382..23725740 [NCBI36]
Chr13:13q12.12		 uncertain significance
GRCh38/hg38 13q12.11-34(chr13:19833130-114298614)x3 copy number gain See cases [RCV000134104] Chr13:19833130..114298614 [GRCh38]
Chr13:20407270..115064089 [GRCh37]
Chr13:19305270..114082191 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q12.12(chr13:22672788-23489498)x3 copy number gain See cases [RCV000051982] Chr13:22672788..23489498 [GRCh38]
Chr13:23246927..24063637 [GRCh37]
Chr13:22144927..22961637 [NCBI36]
Chr13:13q12.12		 uncertain significance
GRCh38/hg38 13q12.12(chr13:22992823-24316005)x1 copy number loss See cases [RCV000051233] Chr13:22992823..24316005 [GRCh38]
Chr13:23566962..24890143 [GRCh37]
Chr13:22464962..23788143 [NCBI36]
Chr13:13q12.12		 uncertain significance
GRCh38/hg38 13q12.12(chr13:22959219-24384434)x3 copy number gain See cases [RCV000140092] Chr13:22959219..24384434 [GRCh38]
Chr13:23533358..24958572 [GRCh37]
Chr13:22431358..23856572 [NCBI36]
Chr13:13q12.12		 uncertain significance
NC_000013.10:g.(?_23667335)_(23869646_?)dup duplication Autosomal recessive limb-girdle muscular dystrophy type 2C [RCV000708028] Chr13:23093196..23295507 [GRCh38]
Chr13:23667335..23869646 [GRCh37]
Chr13:13q12.12		 uncertain significance
GRCh38/hg38 13q12.12(chr13:22822881-23533846)x1 copy number loss See cases [RCV000135940] Chr13:22822881..23533846 [GRCh38]
Chr13:23397020..24107985 [GRCh37]
Chr13:22295020..23005985 [NCBI36]
Chr13:13q12.12		 uncertain significance
GRCh38/hg38 13q12.11-34(chr13:19837395-114327173)x3 copy number gain See cases [RCV000148126] Chr13:19837395..114327173 [GRCh38]
Chr13:20411535..115085141 [GRCh37]
Chr13:19309535..114110750 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q12.12(chr13:22980339-24363444)x3 copy number gain See cases [RCV000051308] Chr13:22980339..24363444 [GRCh38]
Chr13:23554478..24937582 [GRCh37]
Chr13:22452478..23835582 [NCBI36]
Chr13:13q12.12		 uncertain significance
NC_000013.10:g.(?_23667335)_(23985398_?)dup duplication Spastic paraplegia [RCV000537039] Chr13:23093196..23411259 [GRCh38]
Chr13:23667335..23985398 [GRCh37]
Chr13:13q12.12		 uncertain significance
NC_000013.11:g.(?_23093196)_(23411249_?)del deletion Autosomal recessive limb-girdle muscular dystrophy type 2C [RCV001383147]|Spastic paraplegia [RCV000807921] Chr13:23093196..23411249 [GRCh38]
Chr13:23667335..23985388 [GRCh37]
Chr13:13q12.12		 pathogenic
NC_000013.11:g.(?_23093196)_(23368497_?)del deletion Spastic paraplegia [RCV000798822] Chr13:23093196..23368497 [GRCh38]
Chr13:23667335..23942636 [GRCh37]
Chr13:13q12.12		 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 13q12.11-34(chr13:19671934-114340331)x3 copy number gain See cases [RCV000142924] Chr13:19671934..114340331 [GRCh38]
Chr13:20246074..115085141 [GRCh37]
Chr13:19144074..114123908 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q12.12(chr13:22980365-24336546)x3 copy number gain See cases [RCV000139968] Chr13:22980365..24336546 [GRCh38]
Chr13:23554504..24910684 [GRCh37]
Chr13:22452504..23808684 [NCBI36]
Chr13:13q12.12		 uncertain significance
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(chr13:18850545-114327173)x3 copy number gain See cases [RCV000053723] Chr13:18850545..114327173 [GRCh38]
Chr13:19296527..115085141 [GRCh37]
Chr13:18194527..114110750 [NCBI36]
Chr13:13q11-34		 pathogenic
GRCh38/hg38 13q12.12(chr13:22980365-23533846)x1 copy number loss See cases [RCV000137737] Chr13:22980365..23533846 [GRCh38]
Chr13:23554504..24107985 [GRCh37]
Chr13:22452504..23005985 [NCBI36]
Chr13:13q12.12		 uncertain significance
GRCh38/hg38 13q12.12(chr13:22992950-24336636)x1 copy number loss See cases [RCV000134057] Chr13:22992950..24336636 [GRCh38]
Chr13:23567089..24910774 [GRCh37]
Chr13:22465089..23808774 [NCBI36]
Chr13:13q12.12		 uncertain significance
GRCh38/hg38 13q12.12(chr13:22943845-24336546)x3 copy number gain See cases [RCV000139971] Chr13:22943845..24336546 [GRCh38]
Chr13:23517984..24910684 [GRCh37]
Chr13:22415984..23808684 [NCBI36]
Chr13:13q12.12		 uncertain significance
NC_000013.10:g.(?_23667335)_(23985388_?)dup duplication Autosomal recessive limb-girdle muscular dystrophy type 2C [RCV000815274] Chr13:23093196..23411249 [GRCh38]
Chr13:23667335..23985388 [GRCh37]
Chr13:13q12.12		 uncertain significance
GRCh38/hg38 13q12.12(chr13:22943845-23221349)x3 copy number gain See cases [RCV000134426] Chr13:22943845..23221349 [GRCh38]
Chr13:23517984..23795488 [GRCh37]
Chr13:22415984..22693488 [NCBI36]
Chr13:13q12.12		 benign
NC_000013.11:g.(?_23093196)_(23411259_?)del deletion Autosomal recessive limb-girdle muscular dystrophy type 2C [RCV000707933] Chr13:23093196..23411259 [GRCh38]
Chr13:23667335..23985398 [GRCh37]
Chr13:13q12.12		 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 13q12.11-12.13(chr13:19671934-24985872)x1 copy number loss See cases [RCV000143197] Chr13:19671934..24985872 [GRCh38]
Chr13:20246074..25560010 [GRCh37]
Chr13:19144074..24458010 [NCBI36]
Chr13:13q12.11-12.13		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:26
Count of miRNA genes:26
Interacting mature miRNAs:26
Transcripts:ENST00000414345
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
High
Medium 3
Low 2 2 2 3 1 1 2 327 6 1
Below cutoff 27 27 13 5 10 2 82 65 33 11 44 24 3 5 61

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000414345
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1323,169,835 - 23,170,597 (-)Ensembl
RefSeq Acc Id: XR_007063718
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381323,169,829 - 23,170,872 (-)NCBI
Promoters
RGD ID:15096706
Promoter ID:EPDNEWNC_H1528
Type:initiation region
Name:LINC00362_1
Description:long intergenic non-protein coding RNA 362 [Source:HGNCSymbol;Acc:HGNC:42682]
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 AssemblyChrPosition (strand)Source
GRCh381323,170,595 - 23,170,655EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC00362 COSMIC
Ensembl Genes ENSG00000229483 Ensembl
GTEx ENSG00000229483 GTEx
HGNC ID HGNC:42682 ENTREZGENE
Human Proteome Map LINC00362 Human Proteome Map
NCBI Gene LINC00362 ENTREZGENE