LINC02261 (long intergenic non-protein coding RNA 2261) - Rat Genome Database

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Pathways
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Gene: LINC02261 (long intergenic non-protein coding RNA 2261) Homo sapiens
Analyze
Symbol: LINC02261
Name: long intergenic non-protein coding RNA 2261
RGD ID: 12798853
HGNC Page HGNC:53173
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
GRCh38427,217,479 - 27,282,225 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl427,217,479 - 27,282,225 (+)EnsemblGRCh38hg38GRCh38
GRCh37427,219,101 - 27,283,847 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map4p15.2NCBI
HuRef426,556,980 - 26,621,757 (+)NCBIHuRef
CHM1_1427,220,619 - 27,285,394 (+)NCBICHM1_1
T2T-CHM13v2.0427,202,943 - 27,267,713 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:14702039   PMID:25335168  


Genomics

Variants

.
Variants in LINC02261
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4p16.3-15.1(chr4:72555-28066309)x1 copy number loss See cases [RCV000051642] Chr4:72555..28066309 [GRCh38]
Chr4:72447..28067931 [GRCh37]
Chr4:62447..27677029 [NCBI36]
Chr4:4p16.3-15.1		 pathogenic
GRCh38/hg38 4p16.3-15.1(chr4:72555-33130620)x3 copy number gain See cases [RCV000051753] Chr4:72555..33130620 [GRCh38]
Chr4:72447..33132242 [GRCh37]
Chr4:62447..32808637 [NCBI36]
Chr4:4p16.3-15.1		 pathogenic
GRCh38/hg38 4p16.3-14(chr4:85149-38700366)x3 copy number gain See cases [RCV000051757] Chr4:85149..38700366 [GRCh38]
Chr4:85040..38701987 [GRCh37]
Chr4:75040..38378382 [NCBI36]
Chr4:4p16.3-14		 pathogenic
GRCh38/hg38 4p16.3-14(chr4:72555-39477144)x3 copy number gain See cases [RCV000133677] Chr4:72555..39477144 [GRCh38]
Chr4:72447..39478764 [GRCh37]
Chr4:62447..39155159 [NCBI36]
Chr4:4p16.3-14		 pathogenic
GRCh38/hg38 4p15.2(chr4:23862000-27685546)x1 copy number loss See cases [RCV000135404] Chr4:23862000..27685546 [GRCh38]
Chr4:23863623..27687168 [GRCh37]
Chr4:23472721..27296266 [NCBI36]
Chr4:4p15.2		 pathogenic
GRCh38/hg38 4p16.3-12(chr4:36424-47491595)x3 copy number gain See cases [RCV000137261] Chr4:36424..47491595 [GRCh38]
Chr4:36424..47493612 [GRCh37]
Chr4:26424..47188369 [NCBI36]
Chr4:4p16.3-12		 pathogenic
GRCh38/hg38 4p15.32-15.1(chr4:16925022-32113076)x1 copy number loss See cases [RCV000135806] Chr4:16925022..32113076 [GRCh38]
Chr4:16926645..32114698 [GRCh37]
Chr4:16535743..31758596 [NCBI36]
Chr4:4p15.32-15.1		 pathogenic|likely pathogenic
GRCh38/hg38 4p15.33-14(chr4:11399082-38137335) copy number loss 4p partial monosomy syndrome [RCV003155905] Chr4:11399082..38137335 [GRCh38]
Chr4:4p15.33-14		 pathogenic
GRCh38/hg38 4p16.3-11(chr4:1-49062177)x3 copy number gain Neurodevelopmental disorder [RCV003327611] Chr4:1..49062177 [GRCh38]
Chr4:4p16.3-11		 pathogenic
GRCh38/hg38 4p16.3-13(chr4:2904667-42963232)x3 copy number gain Neurodevelopmental disorder [RCV003327612] Chr4:2904667..42963232 [GRCh38]
Chr4:4p16.3-13		 pathogenic
GRCh38/hg38 4p16.3-q12(chr4:85624-57073230)x3 copy number gain Neurodevelopmental disorder [RCV003327613] Chr4:85624..57073230 [GRCh38]
Chr4:4p16.3-q12		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:72
Interacting mature miRNAs:73
Transcripts:ENST00000512873
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 1 1 4 1
Low 28 8 10 5 113 5 70 25 34 20 30 93 2 2 1
Below cutoff 607 302 241 92 227 69 656 381 648 150 569 429 33 186 287 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000512873
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl427,217,479 - 27,282,225 (+)Ensembl
RefSeq Acc Id: NR_125921
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38427,217,479 - 27,282,225 (+)NCBI
CHM1_1427,220,619 - 27,285,394 (+)NCBI
T2T-CHM13v2.0427,202,943 - 27,267,713 (+)NCBI
Sequence:
Promoters
RGD ID:15095757
Promoter ID:EPDNEWNC_H594
Type:initiation region
Name:LINC02261_1
Description:long intergenic non-protein coding RNA 2261 [Source:HGNCSymbol;Acc:HGNC:53173]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38427,217,472 - 27,217,532EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC02261 COSMIC
Ensembl Genes ENSG00000249699 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000512873 ENTREZGENE
GTEx ENSG00000249699 GTEx
HGNC ID HGNC:53173 ENTREZGENE
Human Proteome Map LINC02261 Human Proteome Map
NCBI Gene LINC02261 ENTREZGENE
RNAcentral URS00004E7C50 RNACentral