LINC02239 (long intergenic non-protein coding RNA 2239) - Rat Genome Database

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Gene: LINC02239 (long intergenic non-protein coding RNA 2239) Homo sapiens
Analyze
Symbol: LINC02239
Name: long intergenic non-protein coding RNA 2239
RGD ID: 12789446
HGNC Page HGNC:27969
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
GRCh38524,835,280 - 24,840,583 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl524,835,280 - 24,840,583 (-)EnsemblGRCh38hg38GRCh38
GRCh37524,835,389 - 24,840,692 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera524,721,103 - 24,726,406 (-)NCBICelera
Cytogenetic Map5p14.1NCBI
HuRef524,800,831 - 24,806,132 (-)NCBIHuRef
CHM1_1524,835,174 - 24,840,477 (-)NCBICHM1_1
T2T-CHM13v2.0524,940,470 - 24,945,773 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5p14.2-14.1(chr5:23758689-26287240)x1 copy number loss See cases [RCV000139638] Chr5:23758689..26287240 [GRCh38]
Chr5:23758798..26287349 [GRCh37]
Chr5:23794555..26323106 [NCBI36]
Chr5:5p14.2-14.1
uncertain significance
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 5p15.33-14.1(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 5p15.33-14.1(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 5p15.33-13.3(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 5p15.33-14.1(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 5p15.33-14.1(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 5p15.33-14.1(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-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 5p15.33-14.1(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 5p15.33-13.2(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 5p15.1-14.1(chr5:18379122-26803906)x1 copy number loss See cases [RCV000142584] Chr5:18379122..26803906 [GRCh38]
Chr5:18379231..26804015 [GRCh37]
Chr5:18414988..26839772 [NCBI36]
Chr5:5p15.1-14.1
benign
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 5p14.3-14.1(chr5:23279693-26849830)x1 copy number loss See cases [RCV000053448] Chr5:23279693..26849830 [GRCh38]
Chr5:23279802..26849939 [GRCh37]
Chr5:23315559..26885696 [NCBI36]
Chr5:5p14.3-14.1
pathogenic
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
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:35
Interacting mature miRNAs:35
Transcripts:ENST00000504339
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 1 1 243 1
Below cutoff 16 23 14 2 10 1 34 19 383 5 135 20 1 2 26

Sequence


RefSeq Acc Id: ENST00000504339
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl524,835,280 - 24,840,583 (-)Ensembl
RefSeq Acc Id: NR_037896
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38524,835,280 - 24,840,583 (-)NCBI
CHM1_1524,835,174 - 24,840,477 (-)NCBI
T2T-CHM13v2.0524,940,470 - 24,945,773 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02239 COSMIC
Ensembl Genes ENSG00000248908 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000504339 ENTREZGENE
GTEx ENSG00000248908 GTEx
HGNC ID HGNC:27969 ENTREZGENE
Human Proteome Map LINC02239 Human Proteome Map
NCBI Gene LINC02239 ENTREZGENE
RNAcentral URS000075B245 RNACentral