LINC00901 (long intergenic non-protein coding RNA 901) - Rat Genome Database
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Gene: LINC00901 (long intergenic non-protein coding RNA 901) Homo sapiens
Analyze
Symbol: LINC00901
Name: long intergenic non-protein coding RNA 901
RGD ID: 5144627
Description:
Type: ncrna
RefSeq Status: VALIDATED
Also known as: LSAMP-AS4; TCONS_00005428
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3116,921,431 - 116,932,238 (+)EnsemblGRCh38hg38GRCh38
GRCh383116,921,431 - 116,932,238 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373116,640,278 - 116,651,085 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera3115,048,261 - 115,059,068 (+)NCBI
Cytogenetic Map3q13.31NCBI
HuRef3114,016,182 - 114,026,987 (+)NCBIHuRef
CHM1_13116,603,315 - 116,614,122 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:12477932   PMID:25435812  


Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:212
Count of miRNA genes:209
Interacting mature miRNAs:212
Transcripts:ENST00000487512
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 281
Low 3 2 1 4 3 1 90 3 1 3
Below cutoff 141 90 142 18 60 10 167 72 942 14 103 213 8 54 104

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000487512
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl3116,921,431 - 116,932,238 (+)Ensembl
RefSeq Acc Id: NR_121607
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383116,921,431 - 116,932,238 (+)NCBI
CHM1_13116,603,315 - 116,614,122 (+)NCBI
Sequence:
Promoters
RGD ID:15095654
Promoter ID:EPDNEWNC_H487
Type:initiation region
Name:LINC00901_1
Description:long intergenic non-protein coding RNA 901 [Source:HGNCSymbol;Acc:HGNC:40352]
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
GRCh383116,921,440 - 116,921,500EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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 3q13.31-21.1(chr3:115019074-122513398)x1 copy number loss See cases [RCV000135961] Chr3:115019074..122513398 [GRCh38]
Chr3:114737921..122232245 [GRCh37]
Chr3:116220611..123714935 [NCBI36]
Chr3:3q13.31-21.1
pathogenic
GRCh38/hg38 3q13.31-13.32(chr3:116366433-119033600)x3 copy number gain See cases [RCV000138196] Chr3:116366433..119033600 [GRCh38]
Chr3:116085280..118752447 [GRCh37]
Chr3:117567970..120235137 [NCBI36]
Chr3:3q13.31-13.32
uncertain significance
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 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 3q13.2-13.33(chr3:112520553-120031022)x1 copy number loss See cases [RCV000142725] Chr3:112520553..120031022 [GRCh38]
Chr3:112239400..119749869 [GRCh37]
Chr3:113722090..121232559 [NCBI36]
Chr3:3q13.2-13.33
pathogenic
GRCh38/hg38 3q13.31-13.32(chr3:114734452-118164045)x1 copy number loss See cases [RCV000143674] Chr3:114734452..118164045 [GRCh38]
Chr3:114453299..117882892 [GRCh37]
Chr3:115935989..119365582 [NCBI36]
Chr3:3q13.31-13.32
uncertain significance
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
GRCh38/hg38 3q13.2-13.31(chr3:112168829-117393356)x1 copy number loss See cases [RCV000050766] Chr3:112168829..117393356 [GRCh38]
Chr3:111887676..117112203 [GRCh37]
Chr3:113370366..118594893 [NCBI36]
Chr3:3q13.2-13.31
pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC LINC00901 COSMIC
Ensembl Genes ENSG00000242385 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000487512 ENTREZGENE
GTEx ENSG00000242385 GTEx
HGNC ID HGNC:40352 ENTREZGENE
Human Proteome Map LINC00901 Human Proteome Map
NCBI Gene 100506724 ENTREZGENE
RNAcentral URS00000D505B RNACentral
UniGene Hs.125983 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-06-04 LINC00901  long intergenic non-protein coding RNA 901  LSAMP-AS4  LSAMP antisense RNA 4  Symbol and/or name change 5135510 APPROVED
2012-08-21 LSAMP-AS4  LSAMP antisense RNA 4  LSAMP-AS4  LSAMP antisense RNA 4 (non-protein coding)  Symbol and/or name change 5135510 APPROVED