LINC02215 (long intergenic non-protein coding RNA 2215) - Rat Genome Database

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Gene: LINC02215 (long intergenic non-protein coding RNA 2215) Homo sapiens
Analyze
Symbol: LINC02215
Name: long intergenic non-protein coding RNA 2215
RGD ID: 12743463
HGNC Page HGNC:53082
Description: ASSOCIATED WITH Autism; autistic disorder
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
GRCh385118,596,188 - 118,628,092 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5118,596,188 - 118,628,092 (+)EnsemblGRCh38hg38GRCh38
GRCh375117,931,883 - 117,963,787 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q23.1NCBI
HuRef5113,118,538 - 113,150,773 (+)NCBIHuRef
CHM1_15117,364,484 - 117,396,351 (+)NCBICHM1_1
T2T-CHM13v2.05119,109,215 - 119,141,117 (+)NCBIT2T-CHM13v2.0
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
Autism  (IAGP)
References
Additional References at PubMed
PMID:16344560  


Genomics


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 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 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 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 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 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(chr5:117766849-118700657)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 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 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:55
Count of miRNA genes:55
Interacting mature miRNAs:55
Transcripts:ENST00000503320
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
Low 1 2 10 1 2 2 202 1 1
Below cutoff 111 186 166 88 72 54 258 114 335 42 208 104 34 80 149

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000503320
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5118,596,188 - 118,628,092 (+)Ensembl
RefSeq Acc Id: NR_104998
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385118,596,188 - 118,628,092 (+)NCBI
CHM1_15117,364,484 - 117,396,351 (+)NCBI
T2T-CHM13v2.05119,109,215 - 119,141,117 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02215 COSMIC
Ensembl Genes ENSG00000249128 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000503320 ENTREZGENE
GTEx ENSG00000249128 GTEx
HGNC ID HGNC:53082 ENTREZGENE
Human Proteome Map LINC02215 Human Proteome Map
NCBI Gene LINC02215 ENTREZGENE
RNAcentral URS00002611B6 RNACentral