LINC02201 (long intergenic non-protein coding RNA 2201) - Rat Genome Database

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Gene: LINC02201 (long intergenic non-protein coding RNA 2201) Homo sapiens
Analyze
Symbol: LINC02201
Name: long intergenic non-protein coding RNA 2201
RGD ID: 11667237
HGNC Page HGNC:53067
Description: ASSOCIATED WITH Congenital Lower Urinary Tract Obstruction
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
GRCh385122,628,952 - 122,730,560 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5122,628,952 - 122,730,685 (-)EnsemblGRCh38hg38GRCh38
GRCh375121,964,647 - 122,066,255 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q23.2NCBI
HuRef5117,152,459 - 117,254,004 (-)NCBIHuRef
CHM1_15121,397,255 - 121,498,870 (-)NCBICHM1_1
T2T-CHM13v2.05123,145,816 - 123,247,427 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References
Additional References at PubMed
PMID:28900495  


Genomics

Variants

.
Variants in LINC02201
7 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q23.1-23.2(chr5:120695675-124525372)x1 copy number loss See cases [RCV000051200] Chr5:120695675..124525372 [GRCh38]
Chr5:120031370..123861065 [GRCh37]
Chr5:120059269..123888964 [NCBI36]
Chr5:5q23.1-23.2		 pathogenic
GRCh38/hg38 5q23.2(chr5:122479268-126833168)x1 copy number loss See cases [RCV000136633] Chr5:122479268..126833168 [GRCh38]
Chr5:121814963..126168860 [GRCh37]
Chr5:121842862..126196759 [NCBI36]
Chr5:5q23.2		 uncertain significance
GRCh38/hg38 5q23.1-23.2(chr5:120739630-126823984)x1 copy number loss See cases [RCV000052108] Chr5:120739630..126823984 [GRCh38]
Chr5:120075325..126159676 [GRCh37]
Chr5:120103224..126187575 [NCBI36]
Chr5:5q23.1-23.2		 pathogenic
GRCh38/hg38 5q23.1-23.2(chr5:118854384-122849602)x3 copy number gain See cases [RCV000053291] Chr5:118854384..122849602 [GRCh38]
Chr5:118190079..122185297 [GRCh37]
Chr5:118217978..122213196 [NCBI36]
Chr5:5q23.1-23.2		 uncertain significance
GRCh38/hg38 5q23.1-31.1(chr5:116677122-132686163)x1 copy number loss See cases [RCV000053525] Chr5:116677122..132686163 [GRCh38]
Chr5:116012818..132021855 [GRCh37]
Chr5:116040717..132049754 [NCBI36]
Chr5:5q23.1-31.1		 pathogenic
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2		 pathogenic
GRCh38/hg38 5q22.3-23.2(chr5:114707561-126507744)x1 copy number loss See cases [RCV000134895] Chr5:114707561..126507744 [GRCh38]
Chr5:114043258..125843436 [GRCh37]
Chr5:114071157..125871335 [NCBI36]
Chr5:5q22.3-23.2		 pathogenic
GRCh38/hg38 5q22.1-23.2(chr5:111463016-127193038)x1 copy number loss See cases [RCV000135549] Chr5:111463016..127193038 [GRCh38]
Chr5:110798714..126528730 [GRCh37]
Chr5:110826613..126556629 [NCBI36]
Chr5:5q22.1-23.2		 pathogenic
GRCh38/hg38 5q14.3-23.3(chr5:90374606-128076423)x1 copy number loss See cases [RCV000139893] Chr5:90374606..128076423 [GRCh38]
Chr5:89670423..127412115 [GRCh37]
Chr5:89706179..127440014 [NCBI36]
Chr5:5q14.3-23.3		 pathogenic
GRCh38/hg38 5q21.3-23.2(chr5:108308463-125777797)x1 copy number loss See cases [RCV000143326] Chr5:108308463..125777797 [GRCh38]
Chr5:107644164..125113490 [GRCh37]
Chr5:107672063..125141389 [NCBI36]
Chr5:5q21.3-23.2		 pathogenic
GRCh38/hg38 5q14.3-31.1(chr5:91411708-131319563)x1 copy number loss See cases [RCV000143746] Chr5:91411708..131319563 [GRCh38]
Chr5:90707525..130655256 [GRCh37]
Chr5:90743281..130683155 [NCBI36]
Chr5:5q14.3-31.1		 pathogenic
GRCh38/hg38 5q22.1-23.3(chr5:110687442-130103838)x1 copy number loss See cases [RCV000139235] Chr5:110687442..130103838 [GRCh38]
Chr5:110023143..129439531 [GRCh37]
Chr5:110051042..129467430 [NCBI36]
Chr5:5q22.1-23.3		 pathogenic|uncertain significance
dup(5)(q23.2q23.2) duplication Lower urinary tract obstruction, congenital [RCV001637969] Chr5:5q23.2 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:355
Count of miRNA genes:314
Interacting mature miRNAs:329
Transcripts:ENST00000508992, ENST00000511194, ENST00000514657
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
Medium 1
Low 1 38 1 1 2 318 2 1 1
Below cutoff 301 555 218 22 560 10 1164 211 1078 55 338 391 13 359 850 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000508992
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5122,729,409 - 122,730,685 (-)Ensembl
RefSeq Acc Id: ENST00000511194
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5122,628,952 - 122,730,559 (-)Ensembl
RefSeq Acc Id: ENST00000514657
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5122,699,390 - 122,722,214 (-)Ensembl
RefSeq Acc Id: ENST00000649085
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5122,629,184 - 122,719,515 (-)Ensembl
RefSeq Acc Id: ENST00000656860
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5122,699,633 - 122,730,658 (-)Ensembl
RefSeq Acc Id: ENST00000659891
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5122,699,632 - 122,730,658 (-)Ensembl
RefSeq Acc Id: ENST00000669389
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5122,714,897 - 122,730,641 (-)Ensembl
RefSeq Acc Id: NR_109881
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385122,628,952 - 122,730,560 (-)NCBI
CHM1_15121,397,255 - 121,498,871 (-)NCBI
T2T-CHM13v2.05123,145,816 - 123,247,427 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC02201 COSMIC
Ensembl Genes ENSG00000251538 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000511194 ENTREZGENE
GTEx ENSG00000251538 GTEx
HGNC ID HGNC:53067 ENTREZGENE
Human Proteome Map LINC02201 Human Proteome Map
NCBI Gene LINC02201 ENTREZGENE
RNAcentral URS000075DF69 RNACentral