LINC02257 (long intergenic non-protein coding RNA 2257) - Rat Genome Database

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Gene: LINC02257 (long intergenic non-protein coding RNA 2257) Homo sapiens
Analyze
Symbol: LINC02257
Name: long intergenic non-protein coding RNA 2257
RGD ID: 13208268
HGNC Page HGNC:53159
Description: ASSOCIATED WITH Usher syndrome; INTERACTS WITH O-methyleugenol; 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
GRCh381221,913,645 - 221,978,520 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1221,880,981 - 221,978,523 (-)EnsemblGRCh38hg38GRCh38
GRCh371222,086,987 - 222,151,862 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q41NCBI
CHM1_11223,220,025 - 223,364,167 (-)NCBICHM1_1
T2T-CHM13v2.01221,153,839 - 221,218,680 (-)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:33855069  


Genomics

Variants

.
Variants in LINC02257
6 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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 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 1q41-44(chr1:221902539-248918469)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051875]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051875]|See cases [RCV000051875] Chr1:221902539..248918469 [GRCh38]
Chr1:222075881..249212668 [GRCh37]
Chr1:220142504..247179291 [NCBI36]
Chr1:1q41-44
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 1q32.2-44(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(chr1:220673535-223683512)x1 copy number loss See cases [RCV000135795] Chr1:220673535..223683512 [GRCh38]
Chr1:220846877..223871214 [GRCh37]
Chr1:218913500..221937837 [NCBI36]
Chr1:1q41
pathogenic
GRCh38/hg38 1q32.1-42.12(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
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:245
Count of miRNA genes:218
Interacting mature miRNAs:230
Transcripts:ENST00000412445, ENST00000433576
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 2 14 1 35 13
Low 66 27 34 46 119 29 650 57 112 28 176 270 23 322 178
Below cutoff 513 1034 353 245 738 135 2107 731 910 113 539 578 116 567 1460

Sequence


RefSeq Acc Id: ENST00000412445
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1221,913,648 - 221,978,523 (-)Ensembl
RefSeq Acc Id: ENST00000433576
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1221,880,981 - 221,918,712 (-)Ensembl
RefSeq Acc Id: NR_149057
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381221,913,645 - 221,978,520 (-)NCBI
T2T-CHM13v2.01221,153,839 - 221,218,680 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02257 COSMIC
Ensembl Genes ENSG00000238042 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000412445 ENTREZGENE
GTEx ENSG00000238042 GTEx
HGNC ID HGNC:53159 ENTREZGENE
Human Proteome Map LINC02257 Human Proteome Map
NCBI Gene LINC02257 ENTREZGENE
RNAcentral URS0000BC4493 RNACentral