LINC01205 (long intergenic non-protein coding RNA 1205) - Rat Genome Database

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Gene: LINC01205 (long intergenic non-protein coding RNA 1205) Homo sapiens
Analyze
Symbol: LINC01205
Name: long intergenic non-protein coding RNA 1205
RGD ID: 8157668
HGNC Page HGNC:49636
Description: INTERACTS WITH butan-1-ol
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP11-702L6.4
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383109,409,990 - 109,495,167 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3109,409,990 - 109,723,273 (+)EnsemblGRCh38hg38GRCh38
GRCh373109,128,837 - 109,214,014 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363110,611,527 - 110,696,704 (+)NCBINCBI36Build 36hg18NCBI36
Celera3107,527,845 - 107,612,993 (+)NCBICelera
Cytogenetic Map3q13.13NCBI
HuRef3106,502,972 - 106,588,068 (+)NCBIHuRef
CHM1_13109,093,007 - 109,178,158 (+)NCBICHM1_1
T2T-CHM13v2.03112,130,242 - 112,215,369 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
butan-1-ol  (EXP)

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:12477932   PMID:21348951  


Genomics

Variants

.
Variants in LINC01205
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_109841.1(LINC01205):n.425-5071G>T single nucleotide variant Lung cancer [RCV000092673] Chr3:109471652 [GRCh38]
Chr3:109190499 [GRCh37]
Chr3:3q13.13		 uncertain significance
GRCh38/hg38 3q11.1-13.31(chr3:93819623-116887056)x1 copy number loss See cases [RCV000135320] Chr3:93819623..116887056 [GRCh38]
Chr3:93538467..116605903 [GRCh37]
Chr3:95021157..118088593 [NCBI36]
Chr3:3q11.1-13.31		 pathogenic
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q11.2-13.31(chr3:97795369-115663349)x1 copy number loss See cases [RCV000138186] Chr3:97795369..115663349 [GRCh38]
Chr3:97514213..115382196 [GRCh37]
Chr3:98996903..116864886 [NCBI36]
Chr3:3q11.2-13.31		 pathogenic|uncertain significance
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24		 pathogenic
GRCh38/hg38 3q13.11-13.31(chr3:104621220-116093884)x3 copy number gain See cases [RCV000051722] Chr3:104621220..116093884 [GRCh38]
Chr3:104340064..115812731 [GRCh37]
Chr3:105822754..117295421 [NCBI36]
Chr3:3q13.11-13.31		 pathogenic
GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1 copy number loss See cases [RCV000051543] Chr3:93886671..123216683 [GRCh38]
Chr3:93605515..122935530 [GRCh37]
Chr3:95088205..124418220 [NCBI36]
Chr3:3q11.1-21.1		 pathogenic
GRCh38/hg38 3q13.13-13.31(chr3:108242572-116169331)x1 copy number loss See cases [RCV000051544] Chr3:108242572..116169331 [GRCh38]
Chr3:107961419..115888178 [GRCh37]
Chr3:109444109..117370868 [NCBI36]
Chr3:3q13.13-13.31		 pathogenic
GRCh38/hg38 3q13.11-13.13(chr3:103692220-109605902)x1 copy number loss See cases [RCV000050910] Chr3:103692220..109605902 [GRCh38]
Chr3:103411064..109324749 [GRCh37]
Chr3:104893754..110807439 [NCBI36]
Chr3:3q13.11-13.13		 pathogenic
GRCh38/hg38 3q11.1-21.2(chr3:93979547-124774010)x1 copy number loss Chromosome 3q13.31 deletion syndrome [RCV003327614] Chr3:93979547..124774010 [GRCh38]
Chr3:3q11.1-21.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:101
Count of miRNA genes:97
Interacting mature miRNAs:99
Transcripts:ENST00000489670, ENST00000497996
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 entire extraembryonic component
High
Medium
Low 8 1 11 7 21 8 27 2 1 7 45 40 1 1 3
Below cutoff 138 103 256 201 199 197 345 92 224 81 504 239 10 31 91 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000489670
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3109,410,162 - 109,419,017 (+)Ensembl
RefSeq Acc Id: ENST00000497996
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3109,409,990 - 109,495,167 (+)Ensembl
RefSeq Acc Id: ENST00000652897
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3109,410,027 - 109,420,410 (+)Ensembl
RefSeq Acc Id: ENST00000658412
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3109,410,064 - 109,680,986 (+)Ensembl
RefSeq Acc Id: ENST00000659474
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3109,410,141 - 109,681,451 (+)Ensembl
RefSeq Acc Id: ENST00000661437
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3109,410,112 - 109,439,013 (+)Ensembl
RefSeq Acc Id: ENST00000663929
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3109,410,027 - 109,723,273 (+)Ensembl
RefSeq Acc Id: ENST00000670331
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3109,410,141 - 109,495,188 (+)Ensembl
RefSeq Acc Id: NR_109841
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383109,409,990 - 109,495,167 (+)NCBI
HuRef3106,502,972 - 106,588,068 (+)NCBI
CHM1_13109,093,007 - 109,178,158 (+)NCBI
T2T-CHM13v2.03112,130,242 - 112,215,369 (+)NCBI
Sequence:
RefSeq Acc Id: NR_109842
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383109,409,990 - 109,420,410 (+)NCBI
HuRef3106,502,972 - 106,588,068 (+)NCBI
CHM1_13109,093,007 - 109,103,427 (+)NCBI
T2T-CHM13v2.03112,130,242 - 112,140,663 (+)NCBI
Sequence:
Promoters
RGD ID:15095641
Promoter ID:EPDNEWNC_H480
Type:initiation region
Name:LINC01205_1
Description:long intergenic non-protein coding RNA 1205 [Source:HGNCSymbol;Acc:HGNC:49636]
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
GRCh383109,410,027 - 109,410,087EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01205 COSMIC
Ensembl Genes ENSG00000228980 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000497996 ENTREZGENE
GTEx ENSG00000228980 GTEx
HGNC ID HGNC:49636 ENTREZGENE
Human Proteome Map LINC01205 Human Proteome Map
NCBI Gene LINC01205 ENTREZGENE
RNAcentral URS00001CF2E9 RNACentral
  URS0000D59D37 RNACentral