LINC01655 (long intergenic non-protein coding RNA 1655) - Rat Genome Database

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Gene: LINC01655 (long intergenic non-protein coding RNA 1655) Homo sapiens
Analyze
Symbol: LINC01655
Name: long intergenic non-protein coding RNA 1655
RGD ID: 11563058
HGNC Page HGNC:52443
Description: ASSOCIATED WITH Usher syndrome; INTERACTS WITH sodium arsenite
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
GRCh381221,827,666 - 221,840,666 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1221,819,842 - 221,840,717 (-)EnsemblGRCh38hg38GRCh38
GRCh371222,001,008 - 222,014,008 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q41NCBI
HuRef1192,682,981 - 192,689,362 (-)NCBIHuRef
CHM1_11223,280,133 - 223,286,522 (-)NCBICHM1_1
T2T-CHM13v2.01221,067,844 - 221,080,844 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
LINC01655HumanUsher syndrome  IAGPRGD:134354448554872ClinVar Annotator: match by term: Usher syndromeClinVarPMID:28041643


  
Object Symbol
Species
Term
Qualifier
Evidence
With
Reference
Notes
Source
Original Reference(s)
LINC01655Humansodium arsenite increases expressionEXP 6480464sodium arsenite results in increased expression of LINC01655 mRNACTDPMID:38568856



.

1 to 10 of 13 rows
Name
Type
Condition(s)
Position(s)
Clinical significance
GRCh38/hg38 1q41(chr1:220673535-223683512)x1 copy number loss See cases [RCV000135795] Chr1:220673535..223683512 [GRCh38]
Chr1:220846877..223871214 [GRCh37]
Chr1:218913500..221937837 [NCBI36]
Chr1:1q41		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:207346642-248930485)x3 copy number gain See cases [RCV000143727] Chr1:207346642..248930485 [GRCh38]
Chr1:207519987..249224684 [GRCh37]
Chr1:205586610..247191307 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q41(chr1:215206760-222004068)x1 copy number loss See cases [RCV000148255] Chr1:215206760..222004068 [GRCh38]
Chr1:215380103..222177410 [GRCh37]
Chr1:213446726..220244033 [NCBI36]
Chr1:1q41		 pathogenic
GRCh38/hg38 1q32.1-42.12(chr1:204764914-225408698)x3 copy number gain See cases [RCV000142054] Chr1:204764914..225408698 [GRCh38]
Chr1:204734042..225596400 [GRCh37]
Chr1:203000665..223663023 [NCBI36]
Chr1:1q32.1-42.12		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:209646207-248931113)x3 copy number gain See cases [RCV000051861] Chr1:209646207..248931113 [GRCh38]
Chr1:209819552..249225312 [GRCh37]
Chr1:207886175..247191935 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q41(chr1:215447347-221971832)x3 copy number gain See cases [RCV000051874] Chr1:215447347..221971832 [GRCh38]
Chr1:215620690..222145174 [GRCh37]
Chr1:213687313..220211797 [NCBI36]
Chr1:1q41		 pathogenic
GRCh38/hg38 1q41(chr1:215206760-222004068)x1 copy number loss See cases [RCV000050298] Chr1:215206760..222004068 [GRCh38]
Chr1:215380103..222177410 [GRCh37]
Chr1:213446726..220244033 [NCBI36]
Chr1:1q41		 pathogenic
GRCh38/hg38 1q32.2-44(chr1:209963625-248918469)x3 copy number gain See cases [RCV000134979] Chr1:209963625..248918469 [GRCh38]
Chr1:210136970..249212668 [GRCh37]
Chr1:208203593..247179291 [NCBI36]
Chr1:1q32.2-44		 pathogenic
GRCh38/hg38 1q41-42.13(chr1:221519280-228862141)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053955]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053955]|See cases [RCV000053955] Chr1:221519280..228862141 [GRCh38]
Chr1:221692622..228997888 [GRCh37]
Chr1:219759245..227064511 [NCBI36]
Chr1:1q41-42.13		 pathogenic
GRCh38/hg38 1q32.3-44(chr1:214023812-248918469)x3 copy number gain See cases [RCV000050981] Chr1:214023812..248918469 [GRCh38]
Chr1:214197155..249212668 [GRCh37]
Chr1:212263778..247179291 [NCBI36]
Chr1:1q32.3-44		 pathogenic
1 to 10 of 13 rows

Predicted Target Of
Summary Value
Count of predictions:93
Count of miRNA genes:92
Interacting mature miRNAs:92
Transcripts:ENST00000431729
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.


The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD ID
Symbol
Name
LOD
P Value
Trait
Sub Trait
Chr
Start
Stop
Species
597448926GWAS1545000_Hcolorectal cancer QTL GWAS1545000 (human)2e-11colorectal cancer1221837846221837847Human
596965901GWAS1085420_Hcolorectal cancer QTL GWAS1085420 (human)2e-11colorectal cancer1221837846221837847Human




adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
606 241 809 246 585 188 644 169 357 94 912 1200 1358 21 455 199 645 520 82



Ensembl Acc Id: ENST00000431729
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1221,834,206 - 221,840,717 (-)Ensembl
Ensembl Acc Id: ENST00000665303
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1221,819,842 - 221,840,689 (-)Ensembl
RefSeq Acc Id: NR_125989
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381221,827,666 - 221,840,666 (-)NCBI
CHM1_11223,273,503 - 223,286,503 (-)NCBI
T2T-CHM13v2.01221,067,844 - 221,080,844 (-)NCBI
Sequence:
RGD ID:15095348
Promoter ID:EPDNEWNC_H183
Type:initiation region
Name:LINC01655_1
Description:long intergenic non-protein coding RNA 1655 [Source:HGNCSymbol;Acc:HGNC:52443]
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
GRCh381221,840,707 - 221,840,767EPDNEWNC


1 to 9 of 9 rows
Database
Acc Id
Source(s)
COSMIC LINC01655 COSMIC
Ensembl Genes ENSG00000227925 Ensembl
GTEx ENSG00000227925 GTEx
HGNC ID HGNC:52443 ENTREZGENE
Human Proteome Map LINC01655 Human Proteome Map
NCBI Gene LINC01655 ENTREZGENE
RNAcentral URS0000204966 RNACentral
  URS0000EEFE34 RNACentral
  URS0000EF069D RNACentral
1 to 9 of 9 rows