LINC02474 (long intergenic non-protein coding RNA 2474) - Rat Genome Database

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Gene: LINC02474 (long intergenic non-protein coding RNA 2474) Homo sapiens
Analyze
Symbol: LINC02474
Name: long intergenic non-protein coding RNA 2474
RGD ID: 13208442
HGNC Page HGNC:53417
Description: ASSOCIATED WITH Usher syndrome; INTERACTS WITH sodium arsenite
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: lncSLCC1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381221,966,410 - 221,984,964 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1221,966,341 - 221,984,964 (+)EnsemblGRCh38hg38GRCh38
GRCh371222,139,752 - 222,158,306 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q41NCBI
T2T-CHM13v2.01221,206,572 - 221,225,114 (+)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:29693709   PMID:33602893  


Genomics

Variants

.
Variants in LINC02474
4 total Variants

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 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 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 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 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 1q32.3-44(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(chr1:215447347-221971832)x3 copy number gain See cases [RCV000051874] Chr1:215447347..221971832 [GRCh38]
Chr1:215620690..222145174 [GRCh37]
Chr1:213687313..220211797 [NCBI36]
Chr1:1q41
pathogenic
GRCh38/hg38 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 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(chr1:221979950-223007060)x3 copy number gain See cases [RCV000137718] Chr1:221979950..223007060 [GRCh38]
Chr1:222153292..223180402 [GRCh37]
Chr1:220219915..221247025 [NCBI36]
Chr1:1q41
uncertain significance
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:163
Count of miRNA genes:159
Interacting mature miRNAs:162
Transcripts:ENST00000421147, ENST00000441160
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 1
Medium 25 1 1 3 4 45 4 5 45 28
Low 55 9 8 11 8 134 3 8 14 76 87 8 1
Below cutoff 180 182 83 112 172 38 812 199 297 46 205 453 74 328 437 1

Sequence


RefSeq Acc Id: ENST00000421147
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1221,966,341 - 221,983,143 (+)Ensembl
RefSeq Acc Id: ENST00000441160
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1221,966,410 - 221,984,964 (+)Ensembl
RefSeq Acc Id: NR_149071
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381221,966,410 - 221,984,964 (+)NCBI
T2T-CHM13v2.01221,206,572 - 221,225,114 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02474 COSMIC
Ensembl Genes ENSG00000228437 Ensembl
GTEx ENSG00000228437 GTEx
HGNC ID HGNC:53417 ENTREZGENE
Human Proteome Map LINC02474 Human Proteome Map
NCBI Gene LINC02474 ENTREZGENE
RNAcentral URS0000BC4419 RNACentral