LINC01299 (long intergenic non-protein coding RNA 1299) - Rat Genome Database

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Gene: LINC01299 (long intergenic non-protein coding RNA 1299) Homo sapiens
Analyze
Symbol: LINC01299
Name: long intergenic non-protein coding RNA 1299
RGD ID: 8655330
HGNC Page HGNC:27839
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
GRCh38865,527,008 - 65,562,666 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl865,526,738 - 65,562,781 (-)EnsemblGRCh38hg38GRCh38
GRCh37866,439,243 - 66,474,901 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera862,430,656 - 62,466,322 (-)NCBICelera
Cytogenetic Map8q13.1NCBI
HuRef861,929,197 - 61,964,872 (-)NCBIHuRef
CHM1_1866,493,933 - 66,529,604 (-)NCBICHM1_1
T2T-CHM13v2.0865,952,658 - 65,988,333 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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   PMID:16344560   PMID:23251661  


Genomics

Variants

.
Variants in LINC01299
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_033893.1(LINC01299):n.61+12048C>T single nucleotide variant Lung cancer [RCV000107623] Chr8:65550558 [GRCh38]
Chr8:66462793 [GRCh37]
Chr8:8q13.1		 uncertain significance
GRCh38/hg38 8q11.1-13.2(chr8:46031334-69303787)x3 copy number gain See cases [RCV000133720] Chr8:46031334..69303787 [GRCh38]
Chr8:46942956..70216022 [GRCh37]
Chr8:47062121..70378576 [NCBI36]
Chr8:8q11.1-13.2		 pathogenic
GRCh38/hg38 8q12.1-13.1(chr8:60519222-66659025)x3 copy number gain See cases [RCV000134830] Chr8:60519222..66659025 [GRCh38]
Chr8:61431781..67571260 [GRCh37]
Chr8:61594335..67733814 [NCBI36]
Chr8:8q12.1-13.1		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8q11.1-24.3(chr8:46031340-139285494)x3 copy number gain See cases [RCV000139539] Chr8:46031340..139285494 [GRCh38]
Chr8:46942962..140297737 [GRCh37]
Chr8:47062127..140366919 [NCBI36]
Chr8:8q11.1-24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p21.3-q24.3(chr8:21291522-145070385)x3 copy number gain See cases [RCV000142021] Chr8:21291522..145070385 [GRCh38]
Chr8:21149033..146295771 [GRCh37]
Chr8:21193313..146266575 [NCBI36]
Chr8:8p21.3-q24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000148092] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8q12.1-21.13(chr8:57361243-79170078)x3 copy number gain See cases [RCV000053653] Chr8:57361243..79170078 [GRCh38]
Chr8:58273802..80082313 [GRCh37]
Chr8:58436356..80244868 [NCBI36]
Chr8:8q12.1-21.13		 pathogenic
GRCh38/hg38 8q12.3-21.13(chr8:61691800-82537696)x3 copy number gain See cases [RCV000053654] Chr8:61691800..82537696 [GRCh38]
Chr8:62604359..83449931 [GRCh37]
Chr8:62766913..83612486 [NCBI36]
Chr8:8q12.3-21.13		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:244417-145054775)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053604]|See cases [RCV000053604] Chr8:244417..145054775 [GRCh38]
Chr8:194417..146280161 [GRCh37]
Chr8:184417..146250965 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8q12.3-21.11(chr8:62230636-73227786)x1 copy number loss See cases [RCV000054242] Chr8:62230636..73227786 [GRCh38]
Chr8:63143195..74140021 [GRCh37]
Chr8:63305749..74302575 [NCBI36]
Chr8:8q12.3-21.11		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:124
Count of miRNA genes:122
Interacting mature miRNAs:122
Transcripts:ENST00000520902
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 24 1 2
Low 2 3 4 1 3 1860 5 4 1 1
Below cutoff 412 389 332 83 369 61 953 340 1112 110 606 441 29 281 472 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000520902
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl865,526,738 - 65,562,781 (-)Ensembl
RefSeq Acc Id: NR_033893
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38865,527,008 - 65,562,666 (-)NCBI
HuRef861,929,197 - 61,964,872 (-)NCBI
CHM1_1866,493,933 - 66,529,604 (-)NCBI
T2T-CHM13v2.0865,952,658 - 65,988,333 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01299 COSMIC
Ensembl Genes ENSG00000254081 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000520902 ENTREZGENE
GTEx ENSG00000254081 GTEx
HGNC ID HGNC:27839 ENTREZGENE
Human Proteome Map LINC01299 Human Proteome Map
NCBI Gene LINC01299 ENTREZGENE
RNAcentral URS0000759B1D RNACentral