LINC00210 (long intergenic non-protein coding RNA 210) - Rat Genome Database

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Gene: LINC00210 (long intergenic non-protein coding RNA 210) Homo sapiens
Analyze
Symbol: LINC00210
Name: long intergenic non-protein coding RNA 210
RGD ID: 6769429
HGNC Page HGNC:37458
Description: ASSOCIATED WITH Usher syndrome; INTERACTS WITH Aflatoxin B2 alpha; antirheumatic drug
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: NCRNA00210
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381217,892,900 - 217,920,804 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1217,892,900 - 217,920,804 (+)EnsemblGRCh38hg38GRCh38
GRCh371218,066,242 - 218,094,146 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q41NCBI
HuRef1188,741,674 - 188,769,388 (+)NCBIHuRef
CHM1_11219,338,974 - 219,366,897 (+)NCBICHM1_1
T2T-CHM13v2.01217,133,693 - 217,161,612 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:30341249   PMID:31240707   PMID:32841458   PMID:33015786  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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(chr1:216598114-218007334)x3 copy number gain See cases [RCV000138050] Chr1:216598114..218007334 [GRCh38]
Chr1:216771456..218180676 [GRCh37]
Chr1:214838079..216247299 [NCBI36]
Chr1:1q41
uncertain significance
GRCh38/hg38 1q41(chr1:217558925-218732002)x3 copy number gain See cases [RCV000142313] Chr1:217558925..218732002 [GRCh38]
Chr1:217732267..218905344 [GRCh37]
Chr1:215798890..216971967 [NCBI36]
Chr1:1q41
uncertain significance
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(chr1:207346642-248930485)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 1q32.3-44(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 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 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
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(chr1:216518607-219827290)x1 copy number loss See cases [RCV000053953] Chr1:216518607..219827290 [GRCh38]
Chr1:216691949..220000632 [GRCh37]
Chr1:214758572..218067255 [NCBI36]
Chr1:1q41
pathogenic
GRCh38/hg38 1q41(chr1:217452423-218818361)x1 copy number loss See cases [RCV000053954] Chr1:217452423..218818361 [GRCh38]
Chr1:217625765..218991703 [GRCh37]
Chr1:215692388..217058326 [NCBI36]
Chr1:1q41
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:237
Count of miRNA genes:192
Interacting mature miRNAs:195
Transcripts:ENST00000431637
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
High
Medium 1
Low 1 2 3 17 60 2
Below cutoff 21 38 68 3 16 2 66 24 144 4 335 50 1 7 50

Sequence


RefSeq Acc Id: ENST00000431637
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1217,892,900 - 217,920,804 (+)Ensembl
RefSeq Acc Id: ENST00000659987
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1217,892,901 - 217,920,034 (+)Ensembl
RefSeq Acc Id: NR_048550
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381217,892,900 - 217,920,804 (+)NCBI
GRCh371218,066,242 - 218,094,146 (+)NCBI
HuRef1188,741,674 - 188,769,388 (+)NCBI
CHM1_11219,338,974 - 219,366,897 (+)NCBI
T2T-CHM13v2.01217,133,693 - 217,161,612 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC00210 COSMIC
Ensembl Genes ENSG00000231814 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000431637 ENTREZGENE
GTEx ENSG00000231814 GTEx
HGNC ID HGNC:37458 ENTREZGENE
Human Proteome Map LINC00210 Human Proteome Map
NCBI Gene LINC00210 ENTREZGENE
RNAcentral URS000075EB39 RNACentral