LINC01742 (long intergenic non-protein coding RNA 1742) - Rat Genome Database

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Gene: LINC01742 (long intergenic non-protein coding RNA 1742) Homo sapiens
Analyze
Symbol: LINC01742
Name: long intergenic non-protein coding RNA 1742
RGD ID: 11563955
HGNC Page HGNC:52530
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
GRCh382058,003,904 - 58,004,648 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2058,003,904 - 58,004,648 (+)EnsemblGRCh38hg38GRCh38
GRCh372056,578,960 - 56,579,704 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map20q13.32NCBI
CHM1_12056,480,427 - 56,481,160 (+)NCBICHM1_1
T2T-CHM13v2.02059,783,100 - 59,783,844 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:11329013  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 20q13.2-13.33(chr20:55630597-60941207)x3 copy number gain See cases [RCV000135622] Chr20:55630597..60941207 [GRCh38]
Chr20:54220678..59516263 [GRCh37]
Chr20:53639062..58949658 [NCBI36]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:53236165-64284202)x3 copy number gain See cases [RCV000143584] Chr20:53236165..64284202 [GRCh38]
Chr20:51852704..62915555 [GRCh37]
Chr20:51286111..62385999 [NCBI36]
Chr20:20q13.2-13.33		 likely pathogenic
GRCh38/hg38 20q13.2-13.33(chr20:56198032-64277321)x3 copy number gain See cases [RCV000138035] Chr20:56198032..64277321 [GRCh38]
Chr20:54773088..62908674 [GRCh37]
Chr20:54206495..62379118 [NCBI36]
Chr20:20q13.2-13.33		 pathogenic
GRCh38/hg38 20q13.12-13.33(chr20:44787704-64277321)x3 copy number gain See cases [RCV000053035] Chr20:44787704..64277321 [GRCh38]
Chr20:43416345..62908674 [GRCh37]
Chr20:42849759..62379118 [NCBI36]
Chr20:20q13.12-13.33		 pathogenic
GRCh38/hg38 20q13.2-13.32(chr20:54594888-58190583)x1 copy number loss See cases [RCV000141033] Chr20:54594888..58190583 [GRCh38]
Chr20:53211427..56765639 [GRCh37]
Chr20:52644834..56199045 [NCBI36]
Chr20:20q13.2-13.32		 pathogenic
GRCh38/hg38 20q13.31-13.33(chr20:57229415-64273089)x3 copy number gain See cases [RCV000141347] Chr20:57229415..64273089 [GRCh38]
Chr20:55804471..62904442 [GRCh37]
Chr20:55237878..62374886 [NCBI36]
Chr20:20q13.31-13.33		 pathogenic

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 19
Low 6 15 1 1 5 7 2 2 347 5 1 7
Below cutoff 156 402 110 44 51 8 531 126 186 9 92 167 37 106 365

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000616333
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2058,003,904 - 58,004,648 (+)Ensembl
RefSeq Acc Id: NR_147083
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382058,003,904 - 58,004,648 (+)NCBI
T2T-CHM13v2.02059,783,100 - 59,783,844 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC01742 COSMIC
Ensembl Genes ENSG00000275852 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000616333 ENTREZGENE
GTEx ENSG00000275852 GTEx
HGNC ID HGNC:52530 ENTREZGENE
Human Proteome Map LINC01742 Human Proteome Map
NCBI Gene LINC01742 ENTREZGENE
RNAcentral URS0000767F6C RNACentral