LINC01069 (long intergenic non-protein coding RNA 1069) - Rat Genome Database

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Gene: LINC01069 (long intergenic non-protein coding RNA 1069) Homo sapiens
Analyze
Symbol: LINC01069
Name: long intergenic non-protein coding RNA 1069
RGD ID: 7321929
HGNC Page HGNC:49109
Description: ASSOCIATED WITH chromosome 13q14 deletion syndrome
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP11-318G21.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381377,979,766 - 77,994,773 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1377,979,817 - 77,997,881 (-)EnsemblGRCh38hg38GRCh38
GRCh371378,553,901 - 78,568,908 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map13q22.3NCBI
HuRef1359,254,788 - 59,270,737 (-)NCBIHuRef
CHM1_11378,523,505 - 78,539,488 (-)NCBICHM1_1
T2T-CHM13v2.01377,204,698 - 77,219,706 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:14702039  


Genomics

Variants

.
Variants in LINC01069
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_108076.1(LINC01069):n.160-776T>C single nucleotide variant Lung cancer [RCV000098260] Chr13:77990384 [GRCh38]
Chr13:78564519 [GRCh37]
Chr13:13q22.3		 uncertain significance
GRCh38/hg38 13q12.11-34(chr13:19833130-114298614)x3 copy number gain See cases [RCV000134104] Chr13:19833130..114298614 [GRCh38]
Chr13:20407270..115064089 [GRCh37]
Chr13:19305270..114082191 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q14.11-31.1(chr13:41288493-85137552)x3 copy number gain See cases [RCV000133944] Chr13:41288493..85137552 [GRCh38]
Chr13:41862629..85711687 [GRCh37]
Chr13:40760629..84609688 [NCBI36]
Chr13:13q14.11-31.1		 pathogenic
GRCh38/hg38 13q21.32-31.2(chr13:66320998-87855429)x1 copy number loss See cases [RCV000134874] Chr13:66320998..87855429 [GRCh38]
Chr13:66895130..88507684 [GRCh37]
Chr13:65793131..87305685 [NCBI36]
Chr13:13q21.32-31.2		 pathogenic
GRCh38/hg38 13q21.2-31.1(chr13:60536344-84553188)x1 copy number loss See cases [RCV000134951] Chr13:60536344..84553188 [GRCh38]
Chr13:61110478..85127323 [GRCh37]
Chr13:60008479..84025324 [NCBI36]
Chr13:13q21.2-31.1		 pathogenic
GRCh38/hg38 13q11-34(chr13:18445862-114327173)x1 copy number loss See cases [RCV000135610] Chr13:18445862..114327173 [GRCh38]
Chr13:19020001..115085141 [GRCh37]
Chr13:10098739..114110750 [NCBI36]
Chr13:13q11-34		 pathogenic
GRCh38/hg38 13q14.11-31.1(chr13:41143820-85137552)x1 copy number loss See cases [RCV000136526] Chr13:41143820..85137552 [GRCh38]
Chr13:41717956..85711687 [GRCh37]
Chr13:40615956..84609688 [NCBI36]
Chr13:13q14.11-31.1		 pathogenic
GRCh38/hg38 13q22.3-31.3(chr13:77061780-92460406)x1 copy number loss See cases [RCV000136886] Chr13:77061780..92460406 [GRCh38]
Chr13:77635915..93112659 [GRCh37]
Chr13:76533916..91910660 [NCBI36]
Chr13:13q22.3-31.3		 pathogenic
GRCh38/hg38 13q14.2-31.1(chr13:47117587-84300935)x1 copy number loss See cases [RCV000136647] Chr13:47117587..84300935 [GRCh38]
Chr13:47691722..84875070 [GRCh37]
Chr13:46589723..83773071 [NCBI36]
Chr13:13q14.2-31.1		 pathogenic
GRCh38/hg38 13q14.11-34(chr13:40942298-114340331)x1 copy number loss See cases [RCV000137893] Chr13:40942298..114340331 [GRCh38]
Chr13:41516434..115085141 [GRCh37]
Chr13:40414434..114123908 [NCBI36]
Chr13:13q14.11-34		 pathogenic
GRCh38/hg38 13q13.1-31.1(chr13:32531486-86757044)x3 copy number gain See cases [RCV000138339] Chr13:32531486..86757044 [GRCh38]
Chr13:33105623..87409299 [GRCh37]
Chr13:32003623..86207300 [NCBI36]
Chr13:13q13.1-31.1		 pathogenic
GRCh38/hg38 13q21.33-31.1(chr13:72681540-79638468)x1 copy number loss See cases [RCV000138575] Chr13:72681540..79638468 [GRCh38]
Chr13:73255678..80212603 [GRCh37]
Chr13:72153679..79110604 [NCBI36]
Chr13:13q21.33-31.1		 pathogenic
GRCh38/hg38 13q12.11-34(chr13:19833130-114327106)x3 copy number gain See cases [RCV000139078] Chr13:19833130..114327106 [GRCh38]
Chr13:20407270..115085141 [GRCh37]
Chr13:19305270..114110683 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q11-34(chr13:18456040-114340285)x3 copy number gain See cases [RCV000140004] Chr13:18456040..114340285 [GRCh38]
Chr13:19030180..115105760 [GRCh37]
Chr13:17928180..114123862 [NCBI36]
Chr13:13q11-34		 pathogenic
GRCh38/hg38 13q22.2-31.1(chr13:76530209-78531570)x1 copy number loss See cases [RCV000141902] Chr13:76530209..78531570 [GRCh38]
Chr13:77104344..79105705 [GRCh37]
Chr13:76002345..78003706 [NCBI36]
Chr13:13q22.2-31.1		 pathogenic|uncertain significance
GRCh38/hg38 13q21.31-31.1(chr13:63713365-79638415)x1 copy number loss See cases [RCV000141460] Chr13:63713365..79638415 [GRCh38]
Chr13:64287498..80212550 [GRCh37]
Chr13:63185499..79110551 [NCBI36]
Chr13:13q21.31-31.1		 pathogenic
GRCh38/hg38 13q12.11-34(chr13:19671934-114340331)x3 copy number gain See cases [RCV000142924] Chr13:19671934..114340331 [GRCh38]
Chr13:20246074..115085141 [GRCh37]
Chr13:19144074..114123908 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q22.3-31.1(chr13:77437522-78501976)x3 copy number gain See cases [RCV000143679] Chr13:77437522..78501976 [GRCh38]
Chr13:78011657..79076111 [GRCh37]
Chr13:76909658..77974112 [NCBI36]
Chr13:13q22.3-31.1		 uncertain significance
GRCh38/hg38 13q11-34(chr13:18862146-114342258)x3 copy number gain See cases [RCV000143462] Chr13:18862146..114342258 [GRCh38]
Chr13:19436286..115107733 [GRCh37]
Chr13:18334286..114125835 [NCBI36]
Chr13:13q11-34		 pathogenic
GRCh38/hg38 13q12.3-31.3(chr13:31363472-90575292)x3 copy number gain See cases [RCV000148244] Chr13:31363472..90575292 [GRCh38]
Chr13:31937609..91227546 [GRCh37]
Chr13:30835609..90025547 [NCBI36]
Chr13:13q12.3-31.3		 pathogenic
GRCh38/hg38 13q12.11-34(chr13:19837395-114327173)x3 copy number gain See cases [RCV000148126] Chr13:19837395..114327173 [GRCh38]
Chr13:20411535..115085141 [GRCh37]
Chr13:19309535..114110750 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q14.12-31.3(chr13:44967523-92738168)x1 copy number loss See cases [RCV000050891] Chr13:44967523..92738168 [GRCh38]
Chr13:45541658..93390421 [GRCh37]
Chr13:44439658..92188422 [NCBI36]
Chr13:13q14.12-31.3		 pathogenic
GRCh38/hg38 13q12.3-31.3(chr13:31363472-90575292)x3 copy number gain See cases [RCV000050293] Chr13:31363472..90575292 [GRCh38]
Chr13:31937609..91227546 [GRCh37]
Chr13:30835609..90025547 [NCBI36]
Chr13:13q12.3-31.3		 pathogenic
GRCh38/hg38 13q22.3(chr13:77776013-78349185)x3 copy number gain See cases [RCV000052013] Chr13:77776013..78349185 [GRCh38]
Chr13:78350148..78923320 [GRCh37]
Chr13:77248149..77821321 [NCBI36]
Chr13:13q22.3		 uncertain significance
GRCh38/hg38 13q22.3(chr13:77786162-78345485)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052027]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052027]|See cases [RCV000052027] Chr13:77786162..78345485 [GRCh38]
Chr13:78360297..78919620 [GRCh37]
Chr13:77258298..77817621 [NCBI36]
Chr13:13q22.3		 uncertain significance
GRCh38/hg38 13q12.11-34(chr13:19837395-114327173)x3 copy number gain See cases [RCV000053731] Chr13:19837395..114327173 [GRCh38]
Chr13:20411535..115085141 [GRCh37]
Chr13:19309535..114110750 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q12.3-31.1(chr13:30318913-83610426)x3 copy number gain See cases [RCV000053737] Chr13:30318913..83610426 [GRCh38]
Chr13:30893050..84184561 [GRCh37]
Chr13:29791050..83082562 [NCBI36]
Chr13:13q12.3-31.1		 pathogenic
GRCh38/hg38 13q11-34(chr13:18565048-114327173)x3 copy number gain See cases [RCV000053719] Chr13:18565048..114327173 [GRCh38]
Chr13:19139188..115085141 [GRCh37]
Chr13:18037188..114110750 [NCBI36]
Chr13:13q11-34		 pathogenic
GRCh38/hg38 13q11-34(chr13:18850545-114327173)x3 copy number gain See cases [RCV000053723] Chr13:18850545..114327173 [GRCh38]
Chr13:19296527..115085141 [GRCh37]
Chr13:18194527..114110750 [NCBI36]
Chr13:13q11-34		 pathogenic
GRCh38/hg38 13q12.11-34(chr13:18946182-114304628)x3 copy number gain See cases [RCV000053726] Chr13:18946182..114304628 [GRCh38]
Chr13:19520322..115070103 [GRCh37]
Chr13:18418322..114088205 [NCBI36]
Chr13:13q12.11-34		 pathogenic
GRCh38/hg38 13q13.2-34(chr13:33528097-114327173)x3 copy number gain See cases [RCV000053759] Chr13:33528097..114327173 [GRCh38]
Chr13:34102234..115085141 [GRCh37]
Chr13:33000234..114110750 [NCBI36]
Chr13:13q13.2-34		 pathogenic
GRCh38/hg38 13q14.11-34(chr13:43219125-114327314)x3 copy number gain See cases [RCV000053762] Chr13:43219125..114327314 [GRCh38]
Chr13:43793261..115085141 [GRCh37]
Chr13:42691261..114110891 [NCBI36]
Chr13:13q14.11-34		 pathogenic
GRCh38/hg38 13q14.11-34(chr13:44164751-114327173)x3 copy number gain See cases [RCV000053764] Chr13:44164751..114327173 [GRCh38]
Chr13:44738887..115085141 [GRCh37]
Chr13:43636887..114110750 [NCBI36]
Chr13:13q14.11-34		 pathogenic
GRCh38/hg38 13q14.12-34(chr13:44733046-114327173)x3 copy number gain See cases [RCV000053767] Chr13:44733046..114327173 [GRCh38]
Chr13:45307182..115085141 [GRCh37]
Chr13:44205182..114110750 [NCBI36]
Chr13:13q14.12-34		 pathogenic
GRCh38/hg38 13q21.33-31.1(chr13:71509212-82146085)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053768]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053768]|See cases [RCV000053768] Chr13:71509212..82146085 [GRCh38]
Chr13:72083344..82720220 [GRCh37]
Chr13:70981345..81618221 [NCBI36]
Chr13:13q21.33-31.1		 pathogenic
GRCh38/hg38 13q22.1-34(chr13:74345951-114327314)x3 copy number gain See cases [RCV000053770] Chr13:74345951..114327314 [GRCh38]
Chr13:74920088..115085141 [GRCh37]
Chr13:73818089..114110891 [NCBI36]
Chr13:13q22.1-34		 pathogenic
NC_000013.11:g.46968080_87381985del40413906 deletion Chromosome 13q14 deletion syndrome [RCV000721955] Chr13:46968080..87381985 [GRCh38]
Chr13:13q14.2-31.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:64
Count of miRNA genes:63
Interacting mature miRNAs:64
Transcripts:ENST00000452933
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
High
Medium 256
Low 1 3 4 7 13 3 9 111 6 4 2
Below cutoff 84 246 218 15 38 9 331 100 883 47 91 248 6 240 148

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000452933
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1377,981,738 - 77,997,844 (-)Ensembl
RefSeq Acc Id: ENST00000662401
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1377,981,127 - 77,997,881 (-)Ensembl
RefSeq Acc Id: ENST00000662574
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1377,979,817 - 77,989,459 (-)Ensembl
RefSeq Acc Id: ENST00000665945
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1377,981,064 - 77,997,881 (-)Ensembl
RefSeq Acc Id: ENST00000666633
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1377,987,929 - 77,997,844 (-)Ensembl
RefSeq Acc Id: ENST00000670477
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1377,981,455 - 77,997,844 (-)Ensembl
RefSeq Acc Id: NR_108076
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381377,979,766 - 77,994,773 (-)NCBI
HuRef1359,252,708 - 59,267,682 (-)NCBI
CHM1_11378,521,425 - 78,536,433 (-)NCBI
T2T-CHM13v2.01377,204,698 - 77,219,706 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01069 COSMIC
Ensembl Genes ENSG00000236133 Ensembl
GTEx ENSG00000236133 GTEx
HGNC ID HGNC:49109 ENTREZGENE
Human Proteome Map LINC01069 Human Proteome Map
NCBI Gene LINC01069 ENTREZGENE
RNAcentral URS000075C755 RNACentral