LINC01148 (long intergenic non-protein coding RNA 1148) - Rat Genome Database

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Gene: LINC01148 (long intergenic non-protein coding RNA 1148) Homo sapiens
Analyze
Symbol: LINC01148
Name: long intergenic non-protein coding RNA 1148
RGD ID: 11565291
HGNC Page HGNC:27507
Description: INTERACTS WITH bisphenol A; fulvestrant
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
GRCh381486,905,778 - 86,922,755 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1486,905,778 - 86,922,755 (+)EnsemblGRCh38hg38GRCh38
GRCh371487,372,122 - 87,389,099 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361486,441,872 - 86,458,852 (+)NCBINCBI36Build 36hg18NCBI36
Celera1467,417,944 - 67,434,924 (+)NCBICelera
Cytogenetic Map14q31.3NCBI
HuRef1467,542,056 - 67,559,039 (+)NCBIHuRef
CHM1_11487,310,696 - 87,327,685 (+)NCBICHM1_1
T2T-CHM13v2.01481,126,771 - 81,143,756 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
bisphenol A  (EXP)
fulvestrant  (EXP)

References
Additional References at PubMed
PMID:12477932  


Genomics

Variants

.
Variants in LINC01148
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 14q31.3-32.33(chr14:86094030-106832642)x3 copy number gain See cases [RCV000052295] Chr14:86094030..106832642 [GRCh38]
Chr14:86560374..107240869 [GRCh37]
Chr14:85630127..106311914 [NCBI36]
Chr14:14q31.3-32.33		 pathogenic
GRCh38/hg38 14q24.2-32.2(chr14:72787506-99596719)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052293]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052293]|See cases [RCV000052293] Chr14:72787506..99596719 [GRCh38]
Chr14:73254214..100063056 [GRCh37]
Chr14:72323967..99132809 [NCBI36]
Chr14:14q24.2-32.2		 pathogenic
GRCh38/hg38 14q31.2-32.33(chr14:83912345-106855405)x3 copy number gain See cases [RCV000052294] Chr14:83912345..106855405 [GRCh38]
Chr14:84378689..107263620 [GRCh37]
Chr14:83448442..106334665 [NCBI36]
Chr14:14q31.2-32.33		 pathogenic
GRCh38/hg38 14q24.3-32.33(chr14:73655772-106879298)x3 copy number gain See cases [RCV000134000] Chr14:73655772..106879298 [GRCh38]
Chr14:74122475..107287505 [GRCh37]
Chr14:73192228..106358550 [NCBI36]
Chr14:14q24.3-32.33		 pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20151149-106855263)x3 copy number gain See cases [RCV000135543] Chr14:20151149..106855263 [GRCh38]
Chr14:20619308..107263478 [GRCh37]
Chr14:19689148..106334523 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
GRCh38/hg38 14q31.3(chr14:85815543-87531777)x3 copy number gain See cases [RCV000135783] Chr14:85815543..87531777 [GRCh38]
Chr14:86281887..87998121 [GRCh37]
Chr14:85351640..87067874 [NCBI36]
Chr14:14q31.3		 uncertain significance
GRCh38/hg38 14q31.3(chr14:85536572-86997925)x3 copy number gain See cases [RCV000137844] Chr14:85536572..86997925 [GRCh38]
Chr14:86002916..87464269 [GRCh37]
Chr14:85072669..86534022 [NCBI36]
Chr14:14q31.3		 uncertain significance
GRCh38/hg38 14q31.3(chr14:86155419-88321735)x3 copy number gain See cases [RCV000138221] Chr14:86155419..88321735 [GRCh38]
Chr14:86621763..88788079 [GRCh37]
Chr14:85691516..87857832 [NCBI36]
Chr14:14q31.3		 likely benign
GRCh38/hg38 14q24.3-32.33(chr14:77222795-106879298)x3 copy number gain See cases [RCV000138230] Chr14:77222795..106879298 [GRCh38]
Chr14:77689138..107287505 [GRCh37]
Chr14:76758891..106358550 [NCBI36]
Chr14:14q24.3-32.33		 pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20043514-106877229)x3 copy number gain See cases [RCV000143373] Chr14:20043514..106877229 [GRCh38]
Chr14:20511673..107285437 [GRCh37]
Chr14:19581513..106356482 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:407
Count of miRNA genes:303
Interacting mature miRNAs:322
Transcripts:ENST00000557527
Prediction methods:Miranda
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
Low 2 1 1 2 1 5 292 2 1
Below cutoff 34 22 47 26 95 26 129 40 78 29 139 76 1 2 24 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000557527
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1486,905,778 - 86,922,755 (+)Ensembl
RefSeq Acc Id: NR_038445
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381486,905,778 - 86,922,755 (+)NCBI
CHM1_11487,310,696 - 87,327,685 (+)NCBI
T2T-CHM13v2.01481,126,771 - 81,143,756 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein EAW81354 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences


Additional Information

Database Acc Id Source(s)
COSMIC LINC01148 COSMIC
Ensembl Genes ENSG00000258804 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000557527 ENTREZGENE
GTEx ENSG00000258804 GTEx
HGNC ID HGNC:27507 ENTREZGENE
Human Proteome Map LINC01148 Human Proteome Map
NCBI Gene LINC01148 ENTREZGENE
RNAcentral URS000075B238 RNACentral