LINC02147 (long intergenic non-protein coding RNA 2147) - Rat Genome Database

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Gene: LINC02147 (long intergenic non-protein coding RNA 2147) Homo sapiens
Analyze
Symbol: LINC02147
Name: long intergenic non-protein coding RNA 2147
RGD ID: 11577075
HGNC Page HGNC:53007
Description: ASSOCIATED WITH Autism; autistic disorder; INTERACTS WITH Aflatoxin B2 alpha
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385117,730,361 - 118,266,062 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5117,730,515 - 118,266,267 (+)EnsemblGRCh38hg38GRCh38
GRCh375117,066,056 - 117,601,757 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q23.1NCBI
HuRef5112,441,879 - 112,784,436 (+)NCBIHuRef
CHM1_15116,498,656 - 117,034,340 (+)NCBICHM1_1
T2T-CHM13v2.05118,242,729 - 118,778,606 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Autism  (IAGP)
References
Additional References at PubMed
PMID:11329013   PMID:35906577  


Genomics

Variants

.
Variants in LINC02147
14 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q23.1(chr5:117766849-118700657)x1 copy number loss See cases [RCV000052578] Chr5:117766849..118700657 [GRCh38]
Chr5:117102544..118036352 [GRCh37]
Chr5:117130443..118064251 [NCBI36]
Chr5:5q23.1		 conflicting interpretations of pathogenicity|uncertain significance|conflicting data from submitters
GRCh38/hg38 5q23.1(chr5:116732695-118380159)x3 copy number gain See cases [RCV000053290] Chr5:116732695..118380159 [GRCh38]
Chr5:116068391..117715854 [GRCh37]
Chr5:116096290..117743753 [NCBI36]
Chr5:5q23.1		 uncertain significance
GRCh38/hg38 5q23.1(chr5:117869720-118942213)x1 copy number loss See cases [RCV000140792] Chr5:117869720..118942213 [GRCh38]
Chr5:117205415..118277908 [GRCh37]
Chr5:117233314..118305807 [NCBI36]
Chr5:5q23.1		 uncertain significance
GRCh38/hg38 5q23.1(chr5:117648489-117898236)x1 copy number loss See cases [RCV000141712] Chr5:117648489..117898236 [GRCh38]
Chr5:116984184..117233931 [GRCh37]
Chr5:117012083..117261830 [NCBI36]
Chr5:5q23.1		 uncertain significance
GRCh38/hg38 5q23.1(chr5:117766849-118700657)x1 copy number loss See cases [RCV000148197] Chr5:117766849..118700657 [GRCh38]
Chr5:117102544..118036352 [GRCh37]
Chr5:117130443..118064251 [NCBI36]
Chr5:5q23.1		 uncertain significance
GRCh38/hg38 5q23.1-31.1(chr5:116677122-132686163)x1 copy number loss See cases [RCV000053525] Chr5:116677122..132686163 [GRCh38]
Chr5:116012818..132021855 [GRCh37]
Chr5:116040717..132049754 [NCBI36]
Chr5:5q23.1-31.1		 pathogenic
GRCh38/hg38 5q22.3-23.2(chr5:114707561-126507744)x1 copy number loss See cases [RCV000134895] Chr5:114707561..126507744 [GRCh38]
Chr5:114043258..125843436 [GRCh37]
Chr5:114071157..125871335 [NCBI36]
Chr5:5q22.3-23.2		 pathogenic
GRCh38/hg38 5q22.1-23.2(chr5:111463016-127193038)x1 copy number loss See cases [RCV000135549] Chr5:111463016..127193038 [GRCh38]
Chr5:110798714..126528730 [GRCh37]
Chr5:110826613..126556629 [NCBI36]
Chr5:5q22.1-23.2		 pathogenic
GRCh38/hg38 5q21.3-23.1(chr5:107002209-118025316)x1 copy number loss See cases [RCV000135699] Chr5:107002209..118025316 [GRCh38]
Chr5:106337910..117361011 [GRCh37]
Chr5:106365809..117388910 [NCBI36]
Chr5:5q21.3-23.1		 pathogenic
GRCh38/hg38 5q21.3-23.2(chr5:108308463-125777797)x1 copy number loss See cases [RCV000143326] Chr5:108308463..125777797 [GRCh38]
Chr5:107644164..125113490 [GRCh37]
Chr5:107672063..125141389 [NCBI36]
Chr5:5q21.3-23.2		 pathogenic
GRCh38/hg38 5q14.3-31.1(chr5:91411708-131319563)x1 copy number loss See cases [RCV000143746] Chr5:91411708..131319563 [GRCh38]
Chr5:90707525..130655256 [GRCh37]
Chr5:90743281..130683155 [NCBI36]
Chr5:5q14.3-31.1		 pathogenic
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2		 pathogenic
GRCh38/hg38 5q14.3-23.3(chr5:90374606-128076423)x1 copy number loss See cases [RCV000139893] Chr5:90374606..128076423 [GRCh38]
Chr5:89670423..127412115 [GRCh37]
Chr5:89706179..127440014 [NCBI36]
Chr5:5q14.3-23.3		 pathogenic
GRCh38/hg38 5q22.2-23.1(chr5:112323517-117773507)x1 copy number loss See cases [RCV000140791] Chr5:112323517..117773507 [GRCh38]
Chr5:111659214..117109202 [GRCh37]
Chr5:111687113..117137101 [NCBI36]
Chr5:5q22.2-23.1		 pathogenic
GRCh38/hg38 5q14.3-23.1(chr5:92899734-119614119)x1 copy number loss See cases [RCV000141252] Chr5:92899734..119614119 [GRCh38]
Chr5:92235441..118949814 [GRCh37]
Chr5:92261197..118977713 [NCBI36]
Chr5:5q14.3-23.1		 pathogenic
GRCh38/hg38 5q22.1-23.3(chr5:110687442-130103838)x1 copy number loss See cases [RCV000139235] Chr5:110687442..130103838 [GRCh38]
Chr5:110023143..129439531 [GRCh37]
Chr5:110051042..129467430 [NCBI36]
Chr5:5q22.1-23.3		 pathogenic|uncertain significance
Single allele duplication Autism [RCV000754292] Chr5:114046360..118610426 [GRCh38]
Chr5:5q22.3-23.1		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:60
Interacting mature miRNAs:60
Transcripts:ENST00000509367, ENST00000509669
Prediction methods:Microtar, 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 3 2 1 1
Low 833 276 715 14 229 5 506 582 682 103 641 666 10 256 340
Below cutoff 1343 1540 511 220 368 96 2531 1036 2611 188 563 652 124 856 1572 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000509367
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5117,730,515 - 118,266,267 (+)Ensembl
RefSeq Acc Id: ENST00000509669
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5117,925,008 - 118,206,971 (+)Ensembl
RefSeq Acc Id: ENST00000657852
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5117,730,524 - 118,206,975 (+)Ensembl
RefSeq Acc Id: ENST00000661774
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5117,730,515 - 118,266,256 (+)Ensembl
RefSeq Acc Id: ENST00000666478
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5117,730,574 - 118,206,975 (+)Ensembl
RefSeq Acc Id: ENST00000667067
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5117,760,374 - 118,206,971 (+)Ensembl
RefSeq Acc Id: NR_104997
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385117,730,361 - 118,266,062 (+)NCBI
CHM1_15116,498,656 - 117,034,340 (+)NCBI
T2T-CHM13v2.05118,242,729 - 118,778,606 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02147 COSMIC
Ensembl Genes ENSG00000249797 Ensembl
GTEx ENSG00000249797 GTEx
HGNC ID HGNC:53007 ENTREZGENE
Human Proteome Map LINC02147 Human Proteome Map
NCBI Gene LINC02147 ENTREZGENE
RNAcentral URS000075AC32 RNACentral