LINC02213 (long intergenic non-protein coding RNA 2213) - 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: LINC02213 (long intergenic non-protein coding RNA 2213) Homo sapiens
Analyze
Symbol: LINC02213
Name: long intergenic non-protein coding RNA 2213
RGD ID: 12743383
HGNC Page HGNC:53080
Description:
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
GRCh38510,504,990 - 10,522,084 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl510,504,996 - 10,522,084 (-)EnsemblGRCh38hg38GRCh38
GRCh37510,505,102 - 10,522,196 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5p15.2NCBI
HuRef510,489,225 - 10,493,403 (-)NCBIHuRef
CHM1_1510,504,974 - 10,509,175 (-)NCBICHM1_1
T2T-CHM13v2.0510,444,140 - 10,461,239 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics

Variants

.
Variants in LINC02213
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5p15.31-15.2(chr5:9843412-11298705)x3 copy number gain See cases [RCV000050789] Chr5:9843412..11298705 [GRCh38]
Chr5:9843524..11298817 [GRCh37]
Chr5:9896524..11351817 [NCBI36]
Chr5:5p15.31-15.2		 uncertain significance
GRCh38/hg38 5p15.2-15.1(chr5:10212880-16770474)x3 copy number gain See cases [RCV000136902] Chr5:10212880..16770474 [GRCh38]
Chr5:10212992..16770583 [GRCh37]
Chr5:10265992..16823583 [NCBI36]
Chr5:5p15.2-15.1		 pathogenic
GRCh38/hg38 5p15.33-15.1(chr5:49978-15678451)x1 copy number loss See cases [RCV000050295] Chr5:49978..15678451 [GRCh38]
Chr5:50093..15678560 [GRCh37]
Chr5:103093..15731560 [NCBI36]
Chr5:5p15.33-15.1		 pathogenic
GRCh38/hg38 5p15.33-12(chr5:54839-45649861)x3 copy number gain See cases [RCV000051810] Chr5:54839..45649861 [GRCh38]
Chr5:54954..45649963 [GRCh37]
Chr5:107954..45685720 [NCBI36]
Chr5:5p15.33-12		 pathogenic
GRCh38/hg38 5p15.33-13.2(chr5:54839-35680845)x3 copy number gain See cases [RCV000051811] Chr5:54839..35680845 [GRCh38]
Chr5:54954..35680947 [GRCh37]
Chr5:107954..35716704 [NCBI36]
Chr5:5p15.33-13.2		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-23132046)x1 copy number loss See cases [RCV000053398] Chr5:22149..23132046 [GRCh38]
Chr5:22149..23132155 [GRCh37]
Chr5:75149..23167912 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-15.2(chr5:22149-12004091)x1 copy number loss See cases [RCV000053399] Chr5:22149..12004091 [GRCh38]
Chr5:22149..12004203 [GRCh37]
Chr5:75149..12057203 [NCBI36]
Chr5:5p15.33-15.2		 pathogenic
GRCh38/hg38 5p15.33-15.1(chr5:22149-17425613)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053401]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053401]|See cases [RCV000053401] Chr5:22149..17425613 [GRCh38]
Chr5:22149..17425722 [GRCh37]
Chr5:75149..17478722 [NCBI36]
Chr5:5p15.33-15.1		 pathogenic
GRCh38/hg38 5p15.33-15.1(chr5:22149-15995341)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053418]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053418]|See cases [RCV000053418] Chr5:22149..15995341 [GRCh38]
Chr5:22149..15995450 [GRCh37]
Chr5:75149..16048450 [NCBI36]
Chr5:5p15.33-15.1		 pathogenic
GRCh38/hg38 5p15.33-13.3(chr5:22149-33418188)x3 copy number gain See cases [RCV000133788] Chr5:22149..33418188 [GRCh38]
Chr5:22149..33418294 [GRCh37]
Chr5:75149..33454051 [NCBI36]
Chr5:5p15.33-13.3		 pathogenic
GRCh38/hg38 5p15.33-15.2(chr5:22149-12819999)x1 copy number loss See cases [RCV000133796] Chr5:22149..12819999 [GRCh38]
Chr5:22149..12820111 [GRCh37]
Chr5:75149..12873111 [NCBI36]
Chr5:5p15.33-15.2		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27788616)x1 copy number loss See cases [RCV000134873] Chr5:22149..27788616 [GRCh38]
Chr5:22149..27788723 [GRCh37]
Chr5:75149..27824480 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-11(chr5:49978-46114984)x3 copy number gain See cases [RCV000135453] Chr5:49978..46114984 [GRCh38]
Chr5:50093..46115086 [GRCh37]
Chr5:103093..46150843 [NCBI36]
Chr5:5p15.33-11		 pathogenic
GRCh38/hg38 5p15.33-13.3(chr5:22149-32248010)x1 copy number loss See cases [RCV000135668] Chr5:22149..32248010 [GRCh38]
Chr5:22149..32248116 [GRCh37]
Chr5:75149..32283873 [NCBI36]
Chr5:5p15.33-13.3		 pathogenic
GRCh38/hg38 5p15.33-13.3(chr5:49978-30112535)x1 copy number loss See cases [RCV000135878] Chr5:49978..30112535 [GRCh38]
Chr5:50093..30112642 [GRCh37]
Chr5:103093..30148399 [NCBI36]
Chr5:5p15.33-13.3		 pathogenic
GRCh38/hg38 5p15.33-15.1(chr5:22149-16584575)x1 copy number loss See cases [RCV000136556] Chr5:22149..16584575 [GRCh38]
Chr5:22149..16584684 [GRCh37]
Chr5:75149..16637684 [NCBI36]
Chr5:5p15.33-15.1		 pathogenic
GRCh38/hg38 5p15.33-15.1(chr5:22149-15851376)x3 copy number gain See cases [RCV000136943] Chr5:22149..15851376 [GRCh38]
Chr5:22149..15851485 [GRCh37]
Chr5:75149..15904485 [NCBI36]
Chr5:5p15.33-15.1		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27485619)x1 copy number loss See cases [RCV000137072] Chr5:22149..27485619 [GRCh38]
Chr5:22149..27485726 [GRCh37]
Chr5:75149..27521483 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-28429241)x1 copy number loss See cases [RCV000137165] Chr5:22149..28429241 [GRCh38]
Chr5:22149..28429348 [GRCh37]
Chr5:75149..28465105 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.2(chr5:22149-23607053)x3 copy number gain See cases [RCV000137806] Chr5:22149..23607053 [GRCh38]
Chr5:22149..23607162 [GRCh37]
Chr5:75149..23642919 [NCBI36]
Chr5:5p15.33-14.2		 pathogenic
GRCh38/hg38 5p15.33-15.2(chr5:22149-11429258)x1 copy number loss See cases [RCV000137884] Chr5:22149..11429258 [GRCh38]
Chr5:22149..11429370 [GRCh37]
Chr5:75149..11482370 [NCBI36]
Chr5:5p15.33-15.2		 pathogenic
GRCh38/hg38 5p15.33-15.2(chr5:22149-11530391)x1 copy number loss See cases [RCV000137915] Chr5:22149..11530391 [GRCh38]
Chr5:22149..11530503 [GRCh37]
Chr5:75149..11583503 [NCBI36]
Chr5:5p15.33-15.2		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27187950)x1 copy number loss See cases [RCV000138099] Chr5:22149..27187950 [GRCh38]
Chr5:22149..27188057 [GRCh37]
Chr5:75149..27223814 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-22775295)x1 copy number loss See cases [RCV000138116] Chr5:22149..22775295 [GRCh38]
Chr5:22149..22775404 [GRCh37]
Chr5:75149..22811161 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-21217120)x1 copy number loss See cases [RCV000138553] Chr5:22149..21217120 [GRCh38]
Chr5:22149..21217229 [GRCh37]
Chr5:75149..21252986 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-q13.3(chr5:22149-74412725)x3 copy number gain See cases [RCV000138780] Chr5:22149..74412725 [GRCh38]
Chr5:22149..73708550 [GRCh37]
Chr5:75149..73744306 [NCBI36]
Chr5:5p15.33-q13.3		 pathogenic
GRCh38/hg38 5p15.33-13.2(chr5:22149-35831538)x1 copy number loss See cases [RCV000138888] Chr5:22149..35831538 [GRCh38]
Chr5:22149..35831640 [GRCh37]
Chr5:75149..35867397 [NCBI36]
Chr5:5p15.33-13.2		 pathogenic
GRCh38/hg38 5p15.33-15.1(chr5:22149-16930016)x1 copy number loss See cases [RCV000140964] Chr5:22149..16930016 [GRCh38]
Chr5:22149..16930125 [GRCh37]
Chr5:75149..16983125 [NCBI36]
Chr5:5p15.33-15.1		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-28589192)x1 copy number loss See cases [RCV000141225] Chr5:22149..28589192 [GRCh38]
Chr5:22149..28589299 [GRCh37]
Chr5:75149..28625056 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.32-13.2(chr5:4849498-36818719)x3 copy number gain See cases [RCV000141246] Chr5:4849498..36818719 [GRCh38]
Chr5:4849611..36818821 [GRCh37]
Chr5:4902611..36854578 [NCBI36]
Chr5:5p15.32-13.2		 pathogenic
GRCh38/hg38 5p15.32-14.3(chr5:4932707-18465361)x1 copy number loss See cases [RCV000141795] Chr5:4932707..18465361 [GRCh38]
Chr5:4932820..18465470 [GRCh37]
Chr5:4985820..18501227 [NCBI36]
Chr5:5p15.32-14.3		 pathogenic
GRCh38/hg38 5p15.33-13.2(chr5:113461-33998289)x1 copy number loss See cases [RCV000141844] Chr5:113461..33998289 [GRCh38]
Chr5:113576..33998394 [GRCh37]
Chr5:166576..34034151 [NCBI36]
Chr5:5p15.33-13.2		 pathogenic
GRCh38/hg38 5p15.33-15.2(chr5:113461-14684362)x1 copy number loss See cases [RCV000142183] Chr5:113461..14684362 [GRCh38]
Chr5:113576..14684471 [GRCh37]
Chr5:166576..14737471 [NCBI36]
Chr5:5p15.33-15.2		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-26593891)x1 copy number loss See cases [RCV000142645] Chr5:22149..26593891 [GRCh38]
Chr5:22149..26594000 [GRCh37]
Chr5:75149..26629757 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27611163)x1 copy number loss See cases [RCV000142934] Chr5:22149..27611163 [GRCh38]
Chr5:22149..27611270 [GRCh37]
Chr5:75149..27647027 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-21726360)x1 copy number loss See cases [RCV000143022] Chr5:22149..21726360 [GRCh38]
Chr5:22149..21726469 [GRCh37]
Chr5:75149..21762226 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-15.1(chr5:49978-15678451)x1 copy number loss See cases [RCV000148250] Chr5:49978..15678451 [GRCh38]
Chr5:50093..15678560 [GRCh37]
Chr5:103093..15731560 [NCBI36]
Chr5:5p15.33-15.1		 pathogenic
GRCh38/hg38 5p15.31-15.2(chr5:7670933-13623997)x1 copy number loss See cases [RCV000139904] Chr5:7670933..13623997 [GRCh38]
Chr5:7671046..13624106 [GRCh37]
Chr5:7724046..13677106 [NCBI36]
Chr5:5p15.31-15.2		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22419-19280892)x1 copy number loss See cases [RCV000053419] Chr5:22419..19280892 [GRCh38]
Chr5:22419..19281001 [GRCh37]
Chr5:75419..19316758 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-15.1(chr5:49778-16908798)x1 copy number loss See cases [RCV000053422] Chr5:49778..16908798 [GRCh38]
Chr5:49893..16908907 [GRCh37]
Chr5:102893..16961907 [NCBI36]
Chr5:5p15.33-15.1		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:49778-19125522)x1 copy number loss See cases [RCV000053424] Chr5:49778..19125522 [GRCh38]
Chr5:49893..19125631 [GRCh37]
Chr5:102893..19161388 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:547757-26541238)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053445]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053445]|See cases [RCV000053445] Chr5:547757..26541238 [GRCh38]
Chr5:547872..26541347 [GRCh37]
Chr5:600872..26577104 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-15.1(chr5:2180761-17602433)x1 copy number loss See cases [RCV000053446] Chr5:2180761..17602433 [GRCh38]
Chr5:2180875..17602542 [GRCh37]
Chr5:2233875..17645646 [NCBI36]
Chr5:5p15.33-15.1		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-25699605)x1 copy number loss See cases [RCV000133768] Chr5:22149..25699605 [GRCh38]
Chr5:22149..25699714 [GRCh37]
Chr5:75149..25735471 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.31-15.2(chr5:8824306-14246099)x1 copy number loss See cases [RCV000137141] Chr5:8824306..14246099 [GRCh38]
Chr5:8824418..14246208 [GRCh37]
Chr5:8877418..14299208 [NCBI36]
Chr5:5p15.31-15.2		 pathogenic|uncertain significance
GRCh38/hg38 5p15.33-14.1(chr5:22149-28075106)x3 copy number gain See cases [RCV000137682] Chr5:22149..28075106 [GRCh38]
Chr5:22149..28075213 [GRCh37]
Chr5:75149..28110970 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic|uncertain significance
GRCh38/hg38 5p15.33-15.2(chr5:9999-14320000)x1 copy number loss Micrognathia-recurrent infections-behavioral abnormalities-mild intellectual disability syndrome [RCV003327718] Chr5:9999..14320000 [GRCh38]
Chr5:5p15.33-15.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:681
Count of miRNA genes:447
Interacting mature miRNAs:476
Transcripts:ENST00000504650, ENST00000506021
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
High
Medium
Low 31 35 3 1 233 7
Below cutoff 101 571 103 22 676 16 174 81 459 28 213 285 7 88 107

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000504650
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl510,505,443 - 10,522,084 (-)Ensembl
RefSeq Acc Id: ENST00000506021
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl510,504,996 - 10,509,194 (-)Ensembl
RefSeq Acc Id: NR_134289
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38510,504,990 - 10,522,084 (-)NCBI
CHM1_1510,504,968 - 10,522,028 (-)NCBI
T2T-CHM13v2.0510,444,140 - 10,461,239 (-)NCBI
Sequence:
RefSeq Acc Id: NR_134290
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38510,504,990 - 10,509,194 (-)NCBI
CHM1_1510,504,968 - 10,509,175 (-)NCBI
T2T-CHM13v2.0510,444,140 - 10,448,319 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02213 COSMIC
Ensembl Genes ENSG00000249160 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000506021 ENTREZGENE
GTEx ENSG00000249160 GTEx
HGNC ID HGNC:53080 ENTREZGENE
Human Proteome Map LINC02213 Human Proteome Map
NCBI Gene LINC02213 ENTREZGENE
RNAcentral URS0000A76F69 RNACentral
  URS0000A77841 RNACentral