LINC02273 (long intergenic non-protein coding RNA 2273) - Rat Genome Database

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Gene: LINC02273 (long intergenic non-protein coding RNA 2273) Homo sapiens
Analyze
Symbol: LINC02273
Name: long intergenic non-protein coding RNA 2273
RGD ID: 12798807
HGNC Page HGNC:53188
Description: INTERACTS WITH diuron; lipopolysaccharide; S-(1,2-dichlorovinyl)-L-cysteine
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
GRCh384152,100,753 - 152,104,720 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4152,090,459 - 152,110,157 (+)EnsemblGRCh38hg38GRCh38
GRCh374153,021,905 - 153,025,872 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map4q31.3NCBI
HuRef4148,747,666 - 148,751,653 (+)NCBIHuRef
CHM1_14152,999,836 - 153,003,794 (+)NCBICHM1_1
T2T-CHM13v2.04155,423,860 - 155,427,846 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:31856843  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q31.3-32.1(chr4:151299810-160314050)x1 copy number loss See cases [RCV000135696] Chr4:151299810..160314050 [GRCh38]
Chr4:152220962..161235202 [GRCh37]
Chr4:152440412..161454652 [NCBI36]
Chr4:4q31.3-32.1		 likely pathogenic
GRCh38/hg38 4q31.3(chr4:151956656-152519401)x1 copy number loss See cases [RCV000140236] Chr4:151956656..152519401 [GRCh38]
Chr4:152877808..153440553 [GRCh37]
Chr4:153097258..153660003 [NCBI36]
Chr4:4q31.3		 uncertain significance
GRCh38/hg38 4q22.2-32.3(chr4:92913386-165299707)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051775]|See cases [RCV000051775] Chr4:92913386..165299707 [GRCh38]
Chr4:93834537..166220859 [GRCh37]
Chr4:94053560..166440309 [NCBI36]
Chr4:4q22.2-32.3		 pathogenic
GRCh38/hg38 4q26-35.2(chr4:118065569-190042639)x3 copy number gain See cases [RCV000051785] Chr4:118065569..190042639 [GRCh38]
Chr4:118986724..190828225 [GRCh37]
Chr4:119206172..191200788 [NCBI36]
Chr4:4q26-35.2		 pathogenic
GRCh38/hg38 4q27-35.2(chr4:121518223-190062270)x3 copy number gain See cases [RCV000051786] Chr4:121518223..190062270 [GRCh38]
Chr4:122439378..190828225 [GRCh37]
Chr4:122658828..191220419 [NCBI36]
Chr4:4q27-35.2		 pathogenic
GRCh38/hg38 4q31.21-31.3(chr4:140876253-152186578)x3 copy number gain See cases [RCV000051787] Chr4:140876253..152186578 [GRCh38]
Chr4:141797407..153107730 [GRCh37]
Chr4:142016857..153327180 [NCBI36]
Chr4:4q31.21-31.3		 pathogenic
GRCh38/hg38 4q31.22-34.1(chr4:147317283-173675559)x3 copy number gain See cases [RCV000051788] Chr4:147317283..173675559 [GRCh38]
Chr4:148238435..174596710 [GRCh37]
Chr4:148457885..174833285 [NCBI36]
Chr4:4q31.22-34.1		 pathogenic
GRCh38/hg38 4q31.23-35.2(chr4:148356485-189548183)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051789]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051789]|See cases [RCV000051789] Chr4:148356485..189548183 [GRCh38]
Chr4:149277637..190469337 [GRCh37]
Chr4:149497087..190706331 [NCBI36]
Chr4:4q31.23-35.2		 pathogenic
GRCh38/hg38 4q31.21-35.2(chr4:145042668-189975519)x3 copy number gain See cases [RCV000135845] Chr4:145042668..189975519 [GRCh38]
Chr4:145963820..190828225 [GRCh37]
Chr4:146183270..191133668 [NCBI36]
Chr4:4q31.21-35.2		 pathogenic
GRCh38/hg38 4q31.1-35.2(chr4:138510532-189963195)x3 copy number gain See cases [RCV000136810] Chr4:138510532..189963195 [GRCh38]
Chr4:139431686..190828225 [GRCh37]
Chr4:139651136..191121344 [NCBI36]
Chr4:4q31.1-35.2		 pathogenic
GRCh38/hg38 4q28.3-35.2(chr4:134935616-190036318)x3 copy number gain See cases [RCV000143559] Chr4:134935616..190036318 [GRCh38]
Chr4:135856771..190957473 [GRCh37]
Chr4:136076221..191194467 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic
GRCh38/hg38 4q28.3-35.2(chr4:131985253-190095391)x3 copy number gain See cases [RCV000137721] Chr4:131985253..190095391 [GRCh38]
Chr4:132906408..190828225 [GRCh37]
Chr4:133125858..191250527 [NCBI36]
Chr4:4q28.3-35.2		 pathogenic|likely benign
GRCh38/hg38 4q28.1-35.1(chr4:125432943-185761887)x3 copy number gain See cases [RCV000138578] Chr4:125432943..185761887 [GRCh38]
Chr4:126354098..186683041 [GRCh37]
Chr4:126573548..186920035 [NCBI36]
Chr4:4q28.1-35.1		 pathogenic|likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:414
Count of miRNA genes:342
Interacting mature miRNAs:363
Transcripts:ENST00000499452, ENST00000504144, ENST00000509332
Prediction methods:Miranda, Rnahybrid, Targetscan
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 pharyngeal arch
High
Medium 1 32 2 48
Low 170 698 130 59 1247 58 108 3 24 73 96 270 5 167 21 1
Below cutoff 1550 1515 1092 396 429 266 2681 1225 2565 220 742 1021 132 968 1631 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000499452
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4152,100,818 - 152,104,720 (+)Ensembl
RefSeq Acc Id: ENST00000504144
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4152,100,760 - 152,101,935 (+)Ensembl
RefSeq Acc Id: ENST00000509332
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4152,100,720 - 152,104,720 (+)Ensembl
RefSeq Acc Id: ENST00000651553
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4152,090,459 - 152,104,720 (+)Ensembl
RefSeq Acc Id: ENST00000688143
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4152,100,785 - 152,110,157 (+)Ensembl
RefSeq Acc Id: ENST00000701232
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4152,100,712 - 152,109,892 (+)Ensembl
RefSeq Acc Id: NR_121627
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384152,100,818 - 152,104,720 (+)NCBI
CHM1_14152,999,894 - 153,003,794 (+)NCBI
T2T-CHM13v2.04155,423,925 - 155,427,846 (+)NCBI
Sequence:
RefSeq Acc Id: NR_121628
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384152,100,753 - 152,104,720 (+)NCBI
CHM1_14152,999,829 - 153,003,794 (+)NCBI
T2T-CHM13v2.04155,423,860 - 155,427,846 (+)NCBI
Sequence:
Promoters
RGD ID:15095921
Promoter ID:EPDNEWNC_H654
Type:initiation region
Name:LINC02273_1
Description:long intergenic non-protein coding RNA 2273 [Source:HGNCSymbol;Acc:HGNC:53188]
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
GRCh384152,100,802 - 152,100,862EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC02273 COSMIC
Ensembl Genes ENSG00000245954 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000499452 ENTREZGENE
  ENST00000509332 ENTREZGENE
GTEx ENSG00000245954 GTEx
HGNC ID HGNC:53188 ENTREZGENE
Human Proteome Map LINC02273 Human Proteome Map
NCBI Gene LINC02273 ENTREZGENE
RNAcentral URS0000225922 RNACentral
  URS000075D0B8 RNACentral