LINC02511 (long intergenic non-protein coding RNA 2511) - Rat Genome Database

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Gene: LINC02511 (long intergenic non-protein coding RNA 2511) Homo sapiens
Analyze
Symbol: LINC02511
Name: long intergenic non-protein coding RNA 2511
RGD ID: 12904410
HGNC Page HGNC:53500
Description: INTERACTS WITH aflatoxin B1; benzo[e]pyrene; methapyrilene
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
GRCh384136,795,902 - 137,212,799 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4136,795,919 - 137,212,799 (-)EnsemblGRCh38hg38GRCh38
GRCh374137,717,057 - 138,133,953 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map4q28.3NCBI
CHM1_14137,692,749 - 138,266,475 (-)NCBICHM1_1
T2T-CHM13v2.04140,118,485 - 140,535,741 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Genomics

Variants

.
Variants in LINC02511
9 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 4q28.2-31.21(chr4:128119872-142431375)x1 copy number loss See cases [RCV000051056] Chr4:128119872..142431375 [GRCh38]
Chr4:129041027..143352528 [GRCh37]
Chr4:129260477..143571978 [NCBI36]
Chr4:4q28.2-31.21		 pathogenic
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 4q26-31.21(chr4:116630862-145429900)x1 copy number loss See cases [RCV000053321] Chr4:116630862..145429900 [GRCh38]
Chr4:117552018..146351052 [GRCh37]
Chr4:117771466..146570502 [NCBI36]
Chr4:4q26-31.21		 pathogenic
GRCh38/hg38 4q28.3(chr4:136132427-136796756)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054073]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000054073]|See cases [RCV000054073] Chr4:136132427..136796756 [GRCh38]
Chr4:137053582..137717911 [GRCh37]
Chr4:137273032..137937361 [NCBI36]
Chr4:4q28.3		 uncertain significance
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
Single allele deletion Normal pregnancy [RCV000161360] Chr4:137182159..137269240 [GRCh38]
Chr4:138103313..138190394 [GRCh37]
Chr4:4q28.3		 not provided
GRCh38/hg38 4q28.3(chr4:137183731-137260213)x1 copy number loss See cases [RCV000140388] Chr4:137183731..137260213 [GRCh38]
Chr4:138104885..138181367 [GRCh37]
Chr4:138324335..138400817 [NCBI36]
Chr4:4q28.3		 benign
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:166
Count of miRNA genes:157
Interacting mature miRNAs:159
Transcripts:ENST00000505736, ENST00000512039
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 2 2 2 2 1 5 1
Low 86 89 18 11 13 7 858 76 293 30 17 27 4 600 338
Below cutoff 1028 1349 535 125 133 14 2108 1087 1093 155 601 513 114 546 1553 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000505736
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4136,796,722 - 137,212,799 (-)Ensembl
RefSeq Acc Id: ENST00000512039
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4136,809,069 - 136,921,382 (-)Ensembl
RefSeq Acc Id: ENST00000652184
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4136,796,725 - 137,212,790 (-)Ensembl
RefSeq Acc Id: ENST00000656187
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4137,030,044 - 137,212,788 (-)Ensembl
RefSeq Acc Id: ENST00000656956
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4136,795,919 - 137,212,773 (-)Ensembl
RefSeq Acc Id: ENST00000669794
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl4137,030,252 - 137,212,779 (-)Ensembl
RefSeq Acc Id: NR_149105
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh384136,795,902 - 137,212,799 (-)NCBI
T2T-CHM13v2.04140,118,485 - 140,535,741 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02511 COSMIC
Ensembl Genes ENSG00000248869 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000656956 ENTREZGENE
GTEx ENSG00000248869 GTEx
HGNC ID HGNC:53500 ENTREZGENE
Human Proteome Map LINC02511 Human Proteome Map
NCBI Gene LINC02511 ENTREZGENE
RNAcentral URS0000BC448E RNACentral