LINC01848 (long intergenic non-protein coding RNA 1848) - Rat Genome Database

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Gene: LINC01848 (long intergenic non-protein coding RNA 1848) Homo sapiens
Analyze
Symbol: LINC01848
Name: long intergenic non-protein coding RNA 1848
RGD ID: 11569791
HGNC Page HGNC:52663
Description:
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
GRCh385109,883,182 - 109,884,903 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5109,883,182 - 109,884,751 (+)EnsemblGRCh38hg38GRCh38
GRCh375109,218,883 - 109,220,604 (+)NCBIGRCh37GRCh37hg19GRCh37
Celera5105,159,088 - 105,161,405 (+)NCBICelera
Cytogenetic Map5q21.3NCBI
HuRef5104,391,582 - 104,393,899 (+)NCBIHuRef
CHM1_15108,652,202 - 108,654,519 (+)NCBICHM1_1
T2T-CHM13v2.05110,387,633 - 110,389,354 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:23535033  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q21.1-22.2(chr5:102373396-113594030)x1 copy number loss See cases [RCV000053523] Chr5:102373396..113594030 [GRCh38]
Chr5:101709100..112929727 [GRCh37]
Chr5:101736999..112957626 [NCBI36]
Chr5:5q21.1-22.2		 pathogenic
GRCh38/hg38 5q21.3-23.1(chr5:108585264-116815075)x1 copy number loss See cases [RCV000133813] Chr5:108585264..116815075 [GRCh38]
Chr5:107920965..116150771 [GRCh37]
Chr5:107948864..116178670 [NCBI36]
Chr5:5q21.3-23.1		 pathogenic
GRCh38/hg38 5q21.3-23.1(chr5:107002209-118025316)x1 copy number loss See cases [RCV000135699] Chr5:107002209..118025316 [GRCh38]
Chr5:106337910..117361011 [GRCh37]
Chr5:106365809..117388910 [NCBI36]
Chr5:5q21.3-23.1		 pathogenic
GRCh38/hg38 5q14.3-22.1(chr5:84603580-111435081)x1 copy number loss See cases [RCV000139656] Chr5:84603580..111435081 [GRCh38]
Chr5:83899398..110770779 [GRCh37]
Chr5:83935154..110798678 [NCBI36]
Chr5:5q14.3-22.1		 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 5q14.3-23.1(chr5:92899734-119614119)x1 copy number loss See cases [RCV000141252] Chr5:92899734..119614119 [GRCh38]
Chr5:92235441..118949814 [GRCh37]
Chr5:92261197..118977713 [NCBI36]
Chr5:5q14.3-23.1		 pathogenic
GRCh38/hg38 5q21.3-22.2(chr5:106586078-113006585)x1 copy number loss See cases [RCV000142171] Chr5:106586078..113006585 [GRCh38]
Chr5:105921779..112342282 [GRCh37]
Chr5:105949678..112370181 [NCBI36]
Chr5:5q21.3-22.2		 pathogenic
GRCh38/hg38 5q15-22.2(chr5:93193104-113287795)x1 copy number loss See cases [RCV000143249] Chr5:93193104..113287795 [GRCh38]
Chr5:92528810..112623492 [GRCh37]
Chr5:92554566..112651391 [NCBI36]
Chr5:5q15-22.2		 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 5q13.3-22.1(chr5:74163186-110809453)x3 copy number gain See cases [RCV000051839] Chr5:74163186..110809453 [GRCh38]
Chr5:73459011..110145153 [GRCh37]
Chr5:73494767..110173052 [NCBI36]
Chr5:5q13.3-22.1		 pathogenic
GRCh38/hg38 5q15-22.3(chr5:96454445-114050905)x3 copy number gain See cases [RCV000051841] Chr5:96454445..114050905 [GRCh38]
Chr5:95790149..113386602 [GRCh37]
Chr5:95815905..113414501 [NCBI36]
Chr5:5q15-22.3		 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 5q21.3-22.1(chr5:106547519-110687501)x3 copy number gain See cases [RCV000138127] Chr5:106547519..110687501 [GRCh38]
Chr5:105883220..110023202 [GRCh37]
Chr5:105911119..110051101 [NCBI36]
Chr5:5q21.3-22.1		 likely pathogenic|uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:224
Count of miRNA genes:205
Interacting mature miRNAs:216
Transcripts:ENST00000523446
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 3 3 12 8 19 8 3 4 7 301 16 3
Below cutoff 159 164 169 93 175 83 312 113 242 55 141 151 12 57 224 2

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000523446
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5109,883,182 - 109,884,751 (+)Ensembl
RefSeq Acc Id: NR_033175
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385109,883,182 - 109,884,903 (+)NCBI
CHM1_15108,652,202 - 108,654,519 (+)NCBI
T2T-CHM13v2.05110,387,633 - 110,389,354 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01848 COSMIC
Ensembl Genes ENSG00000254106 Ensembl
GTEx ENSG00000254106 GTEx
HGNC ID HGNC:52663 ENTREZGENE
Human Proteome Map LINC01848 Human Proteome Map
NCBI Gene LINC01848 ENTREZGENE
RNAcentral URS0000ABD806 RNACentral