LINC02642 (long intergenic non-protein coding RNA 2642) - Rat Genome Database

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Gene: LINC02642 (long intergenic non-protein coding RNA 2642) Homo sapiens
Analyze
Symbol: LINC02642
Name: long intergenic non-protein coding RNA 2642
RGD ID: 13830941
HGNC Page HGNC:54124
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
GRCh38107,444,292 - 7,472,849 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl107,444,298 - 7,472,040 (-)EnsemblGRCh38hg38GRCh38
Cytogenetic Map10p14NCBI
CHM1_1107,508,031 - 7,515,299 (-)NCBICHM1_1
T2T-CHM13v2.0107,444,253 - 7,472,832 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 10p15.3-12.1(chr10:90205-26339978)x3 copy number gain See cases [RCV000138428] Chr10:90205..26339978 [GRCh38]
Chr10:224406..26628907 [GRCh37]
Chr10:126145..26668913 [NCBI36]
Chr10:10p15.3-12.1		 pathogenic
GRCh38/hg38 10p15.3-12.31(chr10:69261-19184047)x3 copy number gain See cases [RCV000053507] Chr10:69261..19184047 [GRCh38]
Chr10:224406..19472976 [GRCh37]
Chr10:105201..19512982 [NCBI36]
Chr10:10p15.3-12.31		 pathogenic
GRCh38/hg38 10p15.1-q11.22(chr10:4604734-48074662)x3 copy number gain See cases [RCV000141497] Chr10:4604734..48074662 [GRCh38]
Chr10:4646926..47531169 [GRCh37]
Chr10:4636926..47125152 [NCBI36]
Chr10:10p15.1-q11.22		 benign
GRCh38/hg38 10p15.3-14(chr10:1601172-9203729)x3 copy number gain See cases [RCV000142241] Chr10:1601172..9203729 [GRCh38]
Chr10:1643367..9245692 [GRCh37]
Chr10:1633367..9285698 [NCBI36]
Chr10:10p15.3-14		 likely pathogenic
GRCh38/hg38 10p15.3-13(chr10:54086-13205916)x3 copy number gain See cases [RCV000142292] Chr10:54086..13205916 [GRCh38]
Chr10:100026..13247916 [GRCh37]
Chr10:90026..13287922 [NCBI36]
Chr10:10p15.3-13		 pathogenic
GRCh38/hg38 10p15.3-14(chr10:90421-8442783)x3 copy number gain See cases [RCV000051107] Chr10:90421..8442783 [GRCh38]
Chr10:224406..8484746 [GRCh37]
Chr10:126361..8524752 [NCBI36]
Chr10:10p15.3-14		 pathogenic
GRCh38/hg38 10p14(chr10:7290341-7680744)x1 copy number loss See cases [RCV000136689] Chr10:7290341..7680744 [GRCh38]
Chr10:7332303..7722707 [GRCh37]
Chr10:7372309..7762713 [NCBI36]
Chr10:10p14		 uncertain significance
GRCh38/hg38 10p15.3-13(chr10:70478-13736564)x1 copy number loss See cases [RCV000138960] Chr10:70478..13736564 [GRCh38]
Chr10:224406..13778564 [GRCh37]
Chr10:106418..13818570 [NCBI36]
Chr10:10p15.3-13		 pathogenic
GRCh38/hg38 10p15.3-12.31(chr10:54086-19336980)x1 copy number loss See cases [RCV000143703] Chr10:54086..19336980 [GRCh38]
Chr10:100026..19625909 [GRCh37]
Chr10:90026..19665915 [NCBI36]
Chr10:10p15.3-12.31		 pathogenic|likely pathogenic
GRCh38/hg38 10p14-12.31(chr10:7428770-21587752)x1 copy number loss See cases [RCV000137307] Chr10:7428770..21587752 [GRCh38]
Chr10:7470732..21876681 [GRCh37]
Chr10:7510738..21916687 [NCBI36]
Chr10:10p14-12.31		 pathogenic|uncertain significance
GRCh38/hg38 10p15.1-13(chr10:4802753-16823491)x1 copy number loss See cases [RCV000052500] Chr10:4802753..16823491 [GRCh38]
Chr10:4844945..16865490 [GRCh37]
Chr10:4834945..16905496 [NCBI36]
Chr10:10p15.1-13		 pathogenic
GRCh38/hg38 10p15.3-13(chr10:73856-12815915)x3 copy number gain See cases [RCV000135340] Chr10:73856..12815915 [GRCh38]
Chr10:119796..12857914 [GRCh37]
Chr10:109796..12897920 [NCBI36]
Chr10:10p15.3-13		 pathogenic
GRCh38/hg38 10p15.3-14(chr10:90421-11713049)x3 copy number gain See cases [RCV000135533] Chr10:90421..11713049 [GRCh38]
Chr10:224406..11755048 [GRCh37]
Chr10:126361..11795054 [NCBI36]
Chr10:10p15.3-14		 pathogenic|uncertain significance
GRCh38/hg38 10p15.3-12.2(chr10:90221-22567425)x3 copy number gain See cases [RCV000053508] Chr10:90221..22567425 [GRCh38]
Chr10:224406..22856354 [GRCh37]
Chr10:126161..22896360 [NCBI36]
Chr10:10p15.3-12.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:68
Interacting mature miRNAs:68
Transcripts:ENST00000420395
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 pharyngeal arch
High
Medium 3 47 1
Low 76 10 47 26 601 15 41 7 176 32 59 29 12 3 37 1 1
Below cutoff 806 487 616 172 380 79 741 316 1837 136 418 492 95 327 513 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NR_184107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184108 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184109 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184114 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184119 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184123 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184126 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184129 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184130 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184131 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_184132 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_930628 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_930629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AL139125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068268 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF455202 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000420395
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl107,445,558 - 7,471,942 (-)Ensembl
RefSeq Acc Id: ENST00000660269
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl107,444,340 - 7,471,860 (-)Ensembl
RefSeq Acc Id: ENST00000670632
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl107,444,298 - 7,472,040 (-)Ensembl
RefSeq Acc Id: NR_184107
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,463,309 - 7,472,849 (-)NCBI
T2T-CHM13v2.0107,463,287 - 7,472,832 (-)NCBI
RefSeq Acc Id: NR_184108
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,466,524 - 7,472,849 (-)NCBI
T2T-CHM13v2.0107,466,503 - 7,472,832 (-)NCBI
RefSeq Acc Id: NR_184109
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,444,292 - 7,472,849 (-)NCBI
T2T-CHM13v2.0107,444,253 - 7,472,832 (-)NCBI
RefSeq Acc Id: NR_184114
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,466,524 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,466,503 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184115
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,463,309 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,463,287 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184116
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,463,309 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,463,287 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184117
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,463,309 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,463,287 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184118
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,463,309 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,463,287 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184119
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,463,309 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,463,287 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184122
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,444,292 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,444,253 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184123
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,444,292 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,444,253 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184124
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,444,292 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,444,253 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184125
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,466,524 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,466,503 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184126
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,466,524 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,466,503 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184127
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,466,524 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,466,503 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184128
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,466,524 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,466,503 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184129
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,466,524 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,466,503 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184130
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,466,524 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,466,503 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184131
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,466,524 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,466,503 - 7,472,023 (-)NCBI
RefSeq Acc Id: NR_184132
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38107,466,524 - 7,472,040 (-)NCBI
T2T-CHM13v2.0107,466,503 - 7,472,023 (-)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC LINC02642 COSMIC
Ensembl Genes ENSG00000232591 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000660269 ENTREZGENE
  ENST00000670632 ENTREZGENE
GTEx ENSG00000232591 GTEx
HGNC ID HGNC:54124 ENTREZGENE
Human Proteome Map LINC02642 Human Proteome Map
NCBI Gene LINC02642 ENTREZGENE
RNAcentral URS00026A1A54 RNACentral
  URS00026A1AC0 RNACentral
  URS00026A1B02 RNACentral
  URS00026A1BA2 RNACentral
  URS00026A1BB2 RNACentral
  URS00026A1D3D RNACentral
  URS00026A1E71 RNACentral
  URS00026A1E72 RNACentral
  URS00026A1F2C RNACentral
  URS00026A1F49 RNACentral
  URS00026A204D RNACentral
  URS00026A20FF RNACentral
  URS00026A21D8 RNACentral
  URS00026A232D RNACentral
  URS00026A2345 RNACentral
  URS00026A2364 RNACentral
  URS00026A2415 RNACentral
  URS00026A24FD RNACentral
  URS00026A2579 RNACentral
  URS00026A279D RNACentral