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
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


Disease Annotations     Click to see Annotation Detail View
Usher syndrome  (IAGP)

References

Genomics


Clinical Variants
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
GRCh38/hg38 1q31.1-42.11(chr1:187143981-224299417)x3 copy number gain See cases [RCV000051857] Chr1:187143981..224299417 [GRCh38]
Chr1:187113113..224487119 [GRCh37]
Chr1:185379736..222553742 [NCBI36]
Chr1:1q31.1-42.11
pathogenic
Single allele deletion Usher syndrome [RCV000505151] Chr1:216066818..222607612 [GRCh38]
Chr1:216240159..222780953 [GRCh37]
Chr1:1q41
likely pathogenic
GRCh38/hg38 1q32.2-42.13(chr1:228006998-228061271)x2 copy number loss Orofacial cleft 2 [RCV002481175] Chr1:228006998..228061271 [GRCh38]
Chr1:1q32.2-42.13
association
miRNA Target Status

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.


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 1 1 357 4
Low 49 10 43 32 105 28 263 29 40 31 130 152 6 155 52
Below cutoff 192 367 145 137 252 66 1266 313 415 71 138 362 76 451 757

Sequence


RefSeq Acc Id: ENST00000431729
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1221,834,206 - 221,840,717 (-)Ensembl
RefSeq 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:
Promoters
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

Additional Information

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