LINC02064 (long intergenic non-protein coding RNA 2064) - Rat Genome Database

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Gene: LINC02064 (long intergenic non-protein coding RNA 2064) Homo sapiens
Analyze
Symbol: LINC02064
Name: long intergenic non-protein coding RNA 2064
RGD ID: 11575127
HGNC Page HGNC:52909
Description: INTERACTS WITH avobenzone
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
GRCh38529,380,070 - 29,395,976 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl529,304,305 - 29,396,095 (-)EnsemblGRCh38hg38GRCh38
GRCh37529,380,177 - 29,396,083 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5p13.3NCBI
HuRef529,348,613 - 29,352,856 (-)NCBIHuRef
CHM1_1529,380,023 - 29,384,261 (-)NCBICHM1_1
T2T-CHM13v2.0529,494,216 - 29,510,116 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
avobenzone  (EXP)

References
Additional References at PubMed
PMID:16344560  


Genomics

Variants

.
Variants in LINC02064
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical 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 5p15.33-11(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 5p15.33-13.2(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 5p14.1-q11.1(chr5:26593632-50288555)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051834]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051834]|See cases [RCV000051834] Chr5:26593632..50288555 [GRCh38]
Chr5:26593741..49584389 [GRCh37]
Chr5:26629498..49620146 [NCBI36]
Chr5:5p14.1-q11.1		 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-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 5p15.33-13.3(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 5p15.32-13.2(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 5p13.3-12(chr5:29299893-45899898)x3 copy number gain See cases [RCV003482191] Chr5:29299893..45899898 [GRCh38]
Chr5:5p13.3-12		 likely 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 5p15.33-13.2(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
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:416
Count of miRNA genes:355
Interacting mature miRNAs:366
Transcripts:ENST00000506492, ENST00000507876
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 256
Low 4 3 1 26 1 11 5 5 125 3 3
Below cutoff 49 40 50 22 60 21 96 33 55 23 113 41 1 20 34

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000506492
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,380,069 - 29,395,989 (-)Ensembl
RefSeq Acc Id: ENST00000507876
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,383,104 - 29,389,940 (-)Ensembl
RefSeq Acc Id: ENST00000653940
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,353,756 - 29,395,976 (-)Ensembl
RefSeq Acc Id: ENST00000654073
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,355,753 - 29,395,974 (-)Ensembl
RefSeq Acc Id: ENST00000654399
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,383,186 - 29,395,979 (-)Ensembl
RefSeq Acc Id: ENST00000655290
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,304,412 - 29,395,979 (-)Ensembl
RefSeq Acc Id: ENST00000655577
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,353,756 - 29,395,974 (-)Ensembl
RefSeq Acc Id: ENST00000656393
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,355,845 - 29,396,031 (-)Ensembl
RefSeq Acc Id: ENST00000657377
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,304,564 - 29,395,974 (-)Ensembl
RefSeq Acc Id: ENST00000658307
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,380,069 - 29,395,979 (-)Ensembl
RefSeq Acc Id: ENST00000658396
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,380,069 - 29,396,031 (-)Ensembl
RefSeq Acc Id: ENST00000658621
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,304,308 - 29,396,007 (-)Ensembl
RefSeq Acc Id: ENST00000659199
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,380,063 - 29,396,095 (-)Ensembl
RefSeq Acc Id: ENST00000659417
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,353,756 - 29,395,979 (-)Ensembl
RefSeq Acc Id: ENST00000660483
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,304,427 - 29,395,974 (-)Ensembl
RefSeq Acc Id: ENST00000662266
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,379,645 - 29,396,036 (-)Ensembl
RefSeq Acc Id: ENST00000664538
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,355,829 - 29,395,995 (-)Ensembl
RefSeq Acc Id: ENST00000664589
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,353,756 - 29,395,987 (-)Ensembl
RefSeq Acc Id: ENST00000666312
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,304,305 - 29,396,031 (-)Ensembl
RefSeq Acc Id: ENST00000667811
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,380,063 - 29,396,031 (-)Ensembl
RefSeq Acc Id: ENST00000668096
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,355,828 - 29,396,010 (-)Ensembl
RefSeq Acc Id: ENST00000668326
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,353,756 - 29,395,979 (-)Ensembl
RefSeq Acc Id: ENST00000668461
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,304,542 - 29,396,022 (-)Ensembl
RefSeq Acc Id: ENST00000669028
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,355,841 - 29,395,981 (-)Ensembl
RefSeq Acc Id: ENST00000669150
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,380,069 - 29,396,031 (-)Ensembl
RefSeq Acc Id: ENST00000669258
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,353,756 - 29,396,031 (-)Ensembl
RefSeq Acc Id: ENST00000669821
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,353,756 - 29,395,983 (-)Ensembl
RefSeq Acc Id: ENST00000671200
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl529,354,195 - 29,395,973 (-)Ensembl
RefSeq Acc Id: NR_104628
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38529,380,070 - 29,395,976 (-)NCBI
CHM1_1529,380,022 - 29,395,922 (-)NCBI
T2T-CHM13v2.0529,494,216 - 29,510,116 (-)NCBI
Sequence:
Promoters
RGD ID:15096045
Promoter ID:EPDNEWNC_H711
Type:initiation region
Name:LINC02064_1
Description:long intergenic non-protein coding RNA 2064 [Source:HGNCSymbol;Acc:HGNC:52909]
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
GRCh38529,395,989 - 29,396,049EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC02064 COSMIC
Ensembl Genes ENSG00000248391 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000506492 ENTREZGENE
GTEx ENSG00000248391 GTEx
HGNC ID HGNC:52909 ENTREZGENE
Human Proteome Map LINC02064 Human Proteome Map
NCBI Gene LINC02064 ENTREZGENE
RNAcentral URS000075C5A3 RNACentral