LINC01943 (long intergenic non-protein coding RNA 1943) - Rat Genome Database

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Gene: LINC01943 (long intergenic non-protein coding RNA 1943) Homo sapiens
Analyze
Symbol: LINC01943
Name: long intergenic non-protein coding RNA 1943
RGD ID: 11569139
HGNC Page HGNC:52767
Description: INTERACTS WITH methylisothiazolinone
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LOC101928152; uncharacterized LOC101928152
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38287,439,523 - 87,459,096 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl287,439,523 - 87,459,044 (-)EnsemblGRCh38hg38GRCh38
GRCh37287,666,641 - 87,758,766 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map2p11.2NCBI
CHM1_1287,668,369 - 87,688,100 (-)NCBICHM1_1
T2T-CHM13v2.0287,451,618 - 87,471,191 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p11.2-11.1(chr2:87098178-91884275)x3 copy number gain See cases [RCV000135666] Chr2:87098178..91884275 [GRCh38]
Chr2:87325301..92072301 [GRCh37]
Chr2:87178812..91436028 [NCBI36]
Chr2:2p11.2-11.1		 uncertain significance
GRCh38/hg38 2p11.2(chr2:86797744-87705899)x3 copy number gain See cases [RCV000053656] Chr2:86797744..87705899 [GRCh38]
Chr2:87024867..88005418 [GRCh37]
Chr2:86878378..87786533 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p11.2(chr2:87098178-87705899)x3 copy number gain See cases [RCV000136497] Chr2:87098178..87705899 [GRCh38]
Chr2:87325301..88005418 [GRCh37]
Chr2:87178812..87786533 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p11.2(chr2:87148954-87705899)x1 copy number loss See cases [RCV000148232] Chr2:87148954..87705899 [GRCh38]
Chr2:87376077..88005418 [GRCh37]
Chr2:87229588..87786533 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p11.2(chr2:87148950-87705910)x1 copy number loss See cases [RCV000134778] Chr2:87148950..87705910 [GRCh38]
Chr2:87376073..88005429 [GRCh37]
Chr2:87229584..87786544 [NCBI36]
Chr2:2p11.2		 likely benign
GRCh38/hg38 2p11.2(chr2:87148954-87655401)x1 copy number loss See cases [RCV000137006] Chr2:87148954..87655401 [GRCh38]
Chr2:87376077..87954920 [GRCh37]
Chr2:87229588..87736035 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p11.2(chr2:87148954-87961277)x3 copy number gain See cases [RCV000133840] Chr2:87148954..87961277 [GRCh38]
Chr2:87376077..88260796 [GRCh37]
Chr2:87229588..88041911 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p12-11.2(chr2:77025216-90282666)x3 copy number gain See cases [RCV000134786] Chr2:77025216..90282666 [GRCh38]
Chr2:77252342..91619262 [GRCh37]
Chr2:77105850..90982989 [NCBI36]
Chr2:2p12-11.2		 pathogenic
GRCh38/hg38 2p11.2(chr2:87148954-87705899)x3 copy number gain See cases [RCV000135504] Chr2:87148954..87705899 [GRCh38]
Chr2:87376077..88005418 [GRCh37]
Chr2:87229588..87786533 [NCBI36]
Chr2:2p11.2		 benign|conflicting interpretations of pathogenicity|conflicting data from submitters
GRCh38/hg38 2p11.2(chr2:85014686-88826619)x1 copy number loss See cases [RCV000141948] Chr2:85014686..88826619 [GRCh38]
Chr2:85241809..89126132 [GRCh37]
Chr2:85095320..88907247 [NCBI36]
Chr2:2p11.2		 pathogenic
GRCh38/hg38 2p11.2(chr2:87098204-87705910)x3 copy number gain See cases [RCV000134132] Chr2:87098204..87705910 [GRCh38]
Chr2:87325327..88005429 [GRCh37]
Chr2:87178838..87786544 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p11.2(chr2:87098204-87705910)x1 copy number loss See cases [RCV000134134] Chr2:87098204..87705910 [GRCh38]
Chr2:87325327..88005429 [GRCh37]
Chr2:87178838..87786544 [NCBI36]
Chr2:2p11.2		 benign|likely benign|conflicting data from submitters
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2		 benign
GRCh38/hg38 2p11.2(chr2:87148954-87655401)x3 copy number gain See cases [RCV000137005] Chr2:87148954..87655401 [GRCh38]
Chr2:87376077..87954920 [GRCh37]
Chr2:87229588..87736035 [NCBI36]
Chr2:2p11.2		 conflicting interpretations of pathogenicity|conflicting data from submitters
GRCh38/hg38 2p11.2(chr2:87375475-90282666)x3 copy number gain See cases [RCV000137550] Chr2:87375475..90282666 [GRCh38]
Chr2:87602598..91619262 [GRCh37]
Chr2:87456109..90982989 [NCBI36]
Chr2:2p11.2		 uncertain significance
GRCh38/hg38 2p11.2(chr2:87148954-87705899)x1 copy number loss See cases [RCV000050724] Chr2:87148954..87705899 [GRCh38]
Chr2:87376077..88005418 [GRCh37]
Chr2:87229588..87786533 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p11.2(chr2:87068547-87705910)x1 copy number loss See cases [RCV000138932] Chr2:87068547..87705910 [GRCh38]
Chr2:87295670..88005429 [GRCh37]
Chr2:87149181..87786544 [NCBI36]
Chr2:2p11.2		 likely benign
GRCh38/hg38 2p11.2(chr2:87148950-87705910)x3 copy number gain See cases [RCV000134777] Chr2:87148950..87705910 [GRCh38]
Chr2:87376073..88005429 [GRCh37]
Chr2:87229584..87786544 [NCBI36]
Chr2:2p11.2		 benign|likely benign|conflicting data from submitters
GRCh38/hg38 2p11.2(chr2:87453471-87583817)x1 copy number loss See cases [RCV000138426] Chr2:87453471..87583817 [GRCh38]
Chr2:87752990..87883336 [GRCh37]
Chr2:87534105..87664451 [NCBI36]
Chr2:2p11.2		 likely benign

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 1 1 15 1 1
Low 748 1430 477 60 1123 25 1544 314 291 56 213 998 42 1054 784 2
Below cutoff 1502 1451 937 339 287 220 2306 1502 2325 109 820 404 124 148 1673

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000625410
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl287,439,523 - 87,459,044 (-)Ensembl
RefSeq Acc Id: ENST00000628090
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl287,455,546 - 87,458,963 (-)Ensembl
RefSeq Acc Id: ENST00000629820
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl287,439,842 - 87,445,756 (-)Ensembl
RefSeq Acc Id: NR_187136
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38287,439,523 - 87,459,096 (-)NCBI
T2T-CHM13v2.0287,451,618 - 87,471,191 (-)NCBI
Promoters
RGD ID:15095450
Promoter ID:EPDNEWNC_H282
Type:initiation region
Name:LINC01943_2
Description:long intergenic non-protein coding RNA 1943 [Source:HGNCSymbol;Acc:HGNC:52767]
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
GRCh38287,445,759 - 87,445,819EPDNEWNC
RGD ID:15095449
Promoter ID:EPDNEWNC_H284
Type:initiation region
Name:LINC01943_1
Description:long intergenic non-protein coding RNA 1943 [Source:HGNCSymbol;Acc:HGNC:52767]
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
GRCh38287,459,077 - 87,459,137EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LINC01943 COSMIC
Ensembl Genes ENSG00000280721 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000625410 ENTREZGENE
GTEx ENSG00000280721 GTEx
HGNC ID HGNC:52767 ENTREZGENE
Human Proteome Map LINC01943 Human Proteome Map
NCBI Gene LINC01943 ENTREZGENE
RNAcentral URS00026A1E54 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-04-14 LINC01943  long intergenic non-protein coding RNA 1943  LOC101928152  uncharacterized LOC101928152  Data merged from RGD:38651329 737654 PROVISIONAL