LINC02216 (long intergenic non-protein coding RNA 2216) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: LINC02216 (long intergenic non-protein coding RNA 2216) Homo sapiens
Analyze
Symbol: LINC02216
Name: long intergenic non-protein coding RNA 2216
RGD ID: 12743541
HGNC Page HGNC:53083
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
GRCh385118,575,479 - 118,581,389 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5118,575,575 - 118,581,324 (+)EnsemblGRCh38hg38GRCh38
Cytogenetic Map5q23.1NCBI
CHM1_15117,343,882 - 117,349,692 (+)NCBICHM1_1
T2T-CHM13v2.05119,088,488 - 119,094,402 (+)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

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 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 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 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 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 5q21.3-23.2(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 5q14.3-23.1(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 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 5q22.1-23.3(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:150
Count of miRNA genes:148
Interacting mature miRNAs:150
Transcripts:ENST00000513366
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
Low 3 2 1 11 1 4 1 2 13 227 7 1
Below cutoff 92 81 108 42 106 42 139 85 234 93 230 157 3 17 48 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000513366
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5118,575,575 - 118,581,324 (+)Ensembl
RefSeq Acc Id: NR_183313
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385118,575,479 - 118,581,389 (+)NCBI
T2T-CHM13v2.05119,088,488 - 119,094,402 (+)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC LINC02216 COSMIC
Ensembl Genes ENSG00000249551 Ensembl
GTEx ENSG00000249551 GTEx
HGNC ID HGNC:53083 ENTREZGENE
Human Proteome Map LINC02216 Human Proteome Map
NCBI Gene LINC02216 ENTREZGENE
RNAcentral URS00026A2715 RNACentral