LINC02035 (long intergenic non-protein coding RNA 2035) - Rat Genome Database

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Gene: LINC02035 (long intergenic non-protein coding RNA 2035) Homo sapiens
Analyze
Symbol: LINC02035
Name: long intergenic non-protein coding RNA 2035
RGD ID: 11571598
HGNC Page HGNC:52875
Description: INTERACTS WITH 17beta-estradiol; 2-hydroxypropanoic acid; aristolochic acid A
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: PREDICTED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383122,886,513 - 122,892,416 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3122,886,941 - 122,892,416 (+)EnsemblGRCh38hg38GRCh38
GRCh373122,605,360 - 122,611,263 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363124,088,048 - 124,089,515 (+)NCBINCBI36Build 36hg18NCBI36
Celera3121,015,458 - 121,021,362 (+)NCBICelera
Cytogenetic Map3q21.1NCBI
HuRef3119,978,762 - 119,984,667 (+)NCBIHuRef
CHM1_13122,569,030 - 122,574,933 (+)NCBICHM1_1
T2T-CHM13v2.03125,605,710 - 125,611,614 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Genomics

Variants

.
Variants in LINC02035
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q13.33-21.2(chr3:121644209-125676353)x1 copy number loss See cases [RCV000051569] Chr3:121644209..125676353 [GRCh38]
Chr3:121363056..125395197 [GRCh37]
Chr3:122845746..126877887 [NCBI36]
Chr3:3q13.33-21.2
pathogenic
GRCh38/hg38 3q13.33-21.3(chr3:121925147-126782249)x1 copy number loss See cases [RCV000140814] Chr3:121925147..126782249 [GRCh38]
Chr3:121643994..126501092 [GRCh37]
Chr3:123126684..127983782 [NCBI36]
Chr3:3q13.33-21.3
pathogenic
GRCh38/hg38 3q13.32-21.3(chr3:118673898-126540730)x1 copy number loss See cases [RCV000143695] Chr3:118673898..126540730 [GRCh38]
Chr3:118392745..126259573 [GRCh37]
Chr3:119875435..127742263 [NCBI36]
Chr3:3q13.32-21.3
pathogenic
GRCh38/hg38 3q13.32-21.2(chr3:119117166-125920734)x1 copy number loss See cases [RCV000051546] Chr3:119117166..125920734 [GRCh38]
Chr3:118836013..125639577 [GRCh37]
Chr3:120318703..127122267 [NCBI36]
Chr3:3q13.32-21.2
pathogenic
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29
pathogenic
GRCh38/hg38 3q13.31-21.2(chr3:114122562-124532374)x1 copy number loss See cases [RCV000142009] Chr3:114122562..124532374 [GRCh38]
Chr3:113841409..124251221 [GRCh37]
Chr3:115324099..125733911 [NCBI36]
Chr3:3q13.31-21.2
pathogenic
GRCh38/hg38 3q11.1-24(chr3:93800620-145695381)x3 copy number gain See cases [RCV000142340] Chr3:93800620..145695381 [GRCh38]
Chr3:93519464..145413168 [GRCh37]
Chr3:95002154..146895858 [NCBI36]
Chr3:3q11.1-24
pathogenic
GRCh38/hg38 3q13.2-21.3(chr3:112620977-128734134)x1 copy number loss See cases [RCV000139033] Chr3:112620977..128734134 [GRCh38]
Chr3:112339824..128452977 [GRCh37]
Chr3:113822514..129935667 [NCBI36]
Chr3:3q13.2-21.3
pathogenic
GRCh38/hg38 3q11.1-21.1(chr3:93886671-123216683)x1 copy number loss See cases [RCV000051543] Chr3:93886671..123216683 [GRCh38]
Chr3:93605515..122935530 [GRCh37]
Chr3:95088205..124418220 [NCBI36]
Chr3:3q11.1-21.1
pathogenic
Single allele duplication not specified [RCV002286365] Chr3:122157406..123113479 [GRCh38]
Chr3:3q13.33-21.1
uncertain significance
GRCh38/hg38 3q11.1-21.2(chr3:93979547-124774010)x1 copy number loss Chromosome 3q13.31 deletion syndrome [RCV003327614] Chr3:93979547..124774010 [GRCh38]
Chr3:3q11.1-21.2
pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:117
Count of miRNA genes:116
Interacting mature miRNAs:117
Transcripts:ENST00000610128
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 597 481 44 6 476 4 1144 878 262 18 209 312 2 28 879 2
Low 1833 2470 1665 602 1301 446 3210 1289 3437 397 1238 1295 168 1176 1909 2
Below cutoff 2 33 14 14 170 14 1 26 9 3 1 1

Sequence


RefSeq Acc Id: ENST00000610128
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3122,886,941 - 122,892,416 (+)Ensembl
RefSeq Acc Id: NR_024618
RefSeq Status: PREDICTED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383122,886,513 - 122,892,416 (+)NCBI
CHM1_13122,569,030 - 122,574,933 (+)NCBI
T2T-CHM13v2.03125,605,710 - 125,611,614 (+)NCBI
Sequence:
Promoters
RGD ID:15095650
Promoter ID:EPDNEWNC_H491
Type:initiation region
Name:LINC02035_1
Description:long intergenic non-protein coding RNA 2035 [Source:HGNCSymbol;Acc:HGNC:52875]
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
GRCh383122,886,951 - 122,887,011EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC02035 COSMIC
Ensembl Genes ENSG00000273033 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000610128 ENTREZGENE
GTEx ENSG00000273033 GTEx
HGNC ID HGNC:52875 ENTREZGENE
Human Proteome Map LINC02035 Human Proteome Map
NCBI Gene LINC02035 ENTREZGENE
RNAcentral URS000075DD27 RNACentral