LINC03023 (long intergenic non-protein coding RNA 3023) - Rat Genome Database

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Gene: LINC03023 (long intergenic non-protein coding RNA 3023) Homo sapiens
Analyze
Symbol: LINC03023
Name: long intergenic non-protein coding RNA 3023
RGD ID: 16559604
HGNC Page HGNC:56154
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC015468.1; LOC102467222; uncharacterized LOC102467222
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38820,953,633 - 20,968,938 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl820,953,127 - 20,968,904 (+)EnsemblGRCh38hg38GRCh38
GRCh37820,811,144 - 20,826,449 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map8p21.3NCBI
CHM1_1821,013,327 - 21,028,633 (+)NCBICHM1_1
T2T-CHM13v2.0821,219,988 - 21,235,321 (+)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 8p23.1-12(chr8:12750796-29445409)x3 copy number gain See cases [RCV000053633] Chr8:12750796..29445409 [GRCh38]
Chr8:12608305..29302926 [GRCh37]
Chr8:12652676..29358845 [NCBI36]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.3-21.1(chr8:2475295-27504279)x1 copy number loss See cases [RCV000050297] Chr8:2475295..27504279 [GRCh38]
Chr8:2292235..27361796 [GRCh37]
Chr8:2121457..27417713 [NCBI36]
Chr8:8p23.3-21.1		 pathogenic
GRCh38/hg38 8p23.1-12(chr8:12383584-29033946)x1 copy number loss See cases [RCV000142516] Chr8:12383584..29033946 [GRCh38]
Chr8:12241093..28891463 [GRCh37]
Chr8:12285464..28947382 [NCBI36]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.3-12(chr8:241605-31091074)x3 copy number gain See cases [RCV000138831] Chr8:241605..31091074 [GRCh38]
Chr8:191605..30948590 [GRCh37]
Chr8:181605..31068132 [NCBI36]
Chr8:8p23.3-12		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241605-145054781)x3 copy number gain See cases [RCV000138643] Chr8:241605..145054781 [GRCh38]
Chr8:191605..146280167 [GRCh37]
Chr8:181605..146250971 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12728904-43673207)x3 copy number gain See cases [RCV000148237] Chr8:12728904..43673207 [GRCh38]
Chr8:12586413..43528350 [GRCh37]
Chr8:12630784..43647507 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.1-11.22(chr8:7141697-38695546)x3 copy number gain See cases [RCV000139891] Chr8:7141697..38695546 [GRCh38]
Chr8:6999219..38553064 [GRCh37]
Chr8:6986629..38672221 [NCBI36]
Chr8:8p23.1-11.22		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:208048-145070385)x3 copy number gain See cases [RCV000141808] Chr8:208048..145070385 [GRCh38]
Chr8:158048..146295771 [GRCh37]
Chr8:148048..146266575 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12609975-43673207)x3 copy number gain See cases [RCV000135786] Chr8:12609975..43673207 [GRCh38]
Chr8:12467484..43528350 [GRCh37]
Chr8:12511855..43647507 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.3-21.2(chr8:241605-24656971)x3 copy number gain See cases [RCV000136026] Chr8:241605..24656971 [GRCh38]
Chr8:191605..24514484 [GRCh37]
Chr8:181605..24570374 [NCBI36]
Chr8:8p23.3-21.2		 pathogenic
GRCh38/hg38 8p23.1-12(chr8:12698495-35476082)x3 copy number gain See cases [RCV000138058] Chr8:12698495..35476082 [GRCh38]
Chr8:12556004..35333600 [GRCh37]
Chr8:12600375..35453142 [NCBI36]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.1-11.23(chr8:11851113-37216333)x3 copy number gain See cases [RCV000139549] Chr8:11851113..37216333 [GRCh38]
Chr8:11708622..37073851 [GRCh37]
Chr8:11746031..37193009 [NCBI36]
Chr8:8p23.1-11.23		 pathogenic
GRCh38/hg38 8p23.1-11.21(chr8:12609975-42085703)x3 copy number gain See cases [RCV000148249] Chr8:12609975..42085703 [GRCh38]
Chr8:12467484..41943221 [GRCh37]
Chr8:12511855..42062378 [NCBI36]
Chr8:8p23.1-11.21		 pathogenic
GRCh38/hg38 8p23.3-12(chr8:96310-30614703)x3 copy number gain See cases [RCV000053599] Chr8:96310..30614703 [GRCh38]
Chr8:46310..30472220 [GRCh37]
Chr8:36310..30591762 [NCBI36]
Chr8:8p23.3-12		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145054634)x3 copy number gain See cases [RCV000053602] Chr8:241530..145054634 [GRCh38]
Chr8:191530..146280020 [GRCh37]
Chr8:181530..146250824 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12609975-43336172)x3 copy number gain See cases [RCV000053630] Chr8:12609975..43336172 [GRCh38]
Chr8:12467484..43191315 [GRCh37]
Chr8:12511855..43310472 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12750796-43532444)x3 copy number gain See cases [RCV000053632] Chr8:12750796..43532444 [GRCh38]
Chr8:12608305..43387587 [GRCh37]
Chr8:12652676..43506744 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p22-q11.21(chr8:14940110-47929925)x3 copy number gain See cases [RCV000053635] Chr8:14940110..47929925 [GRCh38]
Chr8:14797619..48842485 [GRCh37]
Chr8:14841990..49005038 [NCBI36]
Chr8:8p22-q11.21		 pathogenic
GRCh38/hg38 8p23.2-21.1(chr8:2475295-27504279)x1 copy number loss See cases [RCV000148252] Chr8:2475295..27504279 [GRCh38]
Chr8:2292235..27361796 [GRCh37]
Chr8:2121457..27417713 [NCBI36]
Chr8:8p23.2-21.1		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12646123-43686843)x3 copy number gain See cases [RCV000139796] Chr8:12646123..43686843 [GRCh38]
Chr8:12503632..43541986 [GRCh37]
Chr8:12548003..43661143 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.1-12(chr8:12725750-30180521)x3 copy number gain See cases [RCV000136825] Chr8:12725750..30180521 [GRCh38]
Chr8:12583259..30038037 [GRCh37]
Chr8:12627630..30157579 [NCBI36]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.3-12(chr8:226452-34491890)x3 copy number gain See cases [RCV000141410] Chr8:226452..34491890 [GRCh38]
Chr8:176452..34349408 [GRCh37]
Chr8:166452..34468950 [NCBI36]
Chr8:8p23.3-12		 pathogenic
GRCh38/hg38 8p23.1-11.21(chr8:12728904-41928741)x3 copy number gain See cases [RCV000051110] Chr8:12728904..41928741 [GRCh38]
Chr8:12586413..41786259 [GRCh37]
Chr8:12630784..41905416 [NCBI36]
Chr8:8p23.1-11.21		 pathogenic
GRCh38/hg38 8p23.1-12(chr8:12383584-36370018)x3 copy number gain See cases [RCV000051145] Chr8:12383584..36370018 [GRCh38]
Chr8:12241093..36227536 [GRCh37]
Chr8:12285464..36347088 [NCBI36]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12728904-43673207)x3 copy number gain See cases [RCV000050912] Chr8:12728904..43673207 [GRCh38]
Chr8:12586413..43528350 [GRCh37]
Chr8:12630784..43647507 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.3-21.3(chr8:241530-23198398)x3 copy number gain See cases [RCV000135967] Chr8:241530..23198398 [GRCh38]
Chr8:191530..23055911 [GRCh37]
Chr8:181530..23111856 [NCBI36]
Chr8:8p23.3-21.3		 pathogenic
GRCh38/hg38 8p23.1-11.21(chr8:12728904-40169194)x3 copy number gain See cases [RCV000136516] Chr8:12728904..40169194 [GRCh38]
Chr8:12586413..40026713 [GRCh37]
Chr8:12630784..40145870 [NCBI36]
Chr8:8p23.1-11.21		 pathogenic
GRCh38/hg38 8p23.1-21.1(chr8:12382844-28625564)x3 copy number gain See cases [RCV000138244] Chr8:12382844..28625564 [GRCh38]
Chr8:12240353..28483081 [GRCh37]
Chr8:12284724..28539000 [NCBI36]
Chr8:8p23.1-21.1		 pathogenic
GRCh38/hg38 8p23.1-11.22(chr8:12729023-39235934)x3 copy number gain See cases [RCV000139770] Chr8:12729023..39235934 [GRCh38]
Chr8:12586532..39093453 [GRCh37]
Chr8:12630903..39212610 [NCBI36]
Chr8:8p23.1-11.22		 pathogenic
GRCh38/hg38 8p23.3-11.23(chr8:226452-38021728)x3 copy number gain See cases [RCV000137807] Chr8:226452..38021728 [GRCh38]
Chr8:176452..37879246 [GRCh37]
Chr8:166452..37998403 [NCBI36]
Chr8:8p23.3-11.23		 pathogenic|likely pathogenic
GRCh38/hg38 8p22-12(chr8:18972996-33619264)x1 copy number loss See cases [RCV000142747] Chr8:18972996..33619264 [GRCh38]
Chr8:18830506..33476782 [GRCh37]
Chr8:18874786..33596324 [NCBI36]
Chr8:8p22-12		 pathogenic
GRCh38/hg38 8p23.1-11.21(chr8:12609975-42085703)x3 copy number gain See cases [RCV000050294] Chr8:12609975..42085703 [GRCh38]
Chr8:12467484..41943221 [GRCh37]
Chr8:12511855..42062378 [NCBI36]
Chr8:8p23.1-11.21		 pathogenic
GRCh38/hg38 8p23.1-11.23(chr8:12609975-37892000)x3 copy number gain See cases [RCV000053629] Chr8:12609975..37892000 [GRCh38]
Chr8:12467484..37749518 [GRCh37]
Chr8:12511855..37868676 [NCBI36]
Chr8:8p23.1-11.23		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12182421-43673207)x3 copy number gain See cases [RCV000137249] Chr8:12182421..43673207 [GRCh38]
Chr8:12039930..43528350 [GRCh37]
Chr8:12077339..43647507 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.1-11.21(chr8:12633490-40685533)x3 copy number gain See cases [RCV000143508] Chr8:12633490..40685533 [GRCh38]
Chr8:12490999..40543052 [GRCh37]
Chr8:12535370..40662209 [NCBI36]
Chr8:8p23.1-11.21		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:226452-145068712)x3 copy number gain See cases [RCV000142858] Chr8:226452..145068712 [GRCh38]
Chr8:176452..146294098 [GRCh37]
Chr8:166452..146264902 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.1-11.1(chr8:12383584-43673207)x3 copy number gain See cases [RCV000135566] Chr8:12383584..43673207 [GRCh38]
Chr8:12241093..43528350 [GRCh37]
Chr8:12285464..43647507 [NCBI36]
Chr8:8p23.1-11.1		 pathogenic
GRCh38/hg38 8p23.3-q24.3(chr8:241530-145049449)x3 copy number gain See cases [RCV000051206] Chr8:241530..145049449 [GRCh38]
Chr8:191530..146274835 [GRCh37]
Chr8:181530..146245639 [NCBI36]
Chr8:8p23.3-q24.3		 pathogenic
GRCh38/hg38 8p23.1-12(chr8:12721809-30183737)x1 copy number loss Microcephaly [RCV003327707] Chr8:12721809..30183737 [GRCh38]
Chr8:8p23.1-12		 pathogenic
GRCh38/hg38 8p23.3-21.2(chr8:449893-23854904)x1 copy number loss Neurodevelopmental disorder [RCV003327729] Chr8:449893..23854904 [GRCh38]
Chr8:8p23.3-21.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:333
Count of miRNA genes:297
Interacting mature miRNAs:305
Transcripts:ENST00000523035, ENST00000523852
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
High
Medium 1 217
Low 1 168 161 5 161 13 3 166 26 12
Below cutoff 114 113 360 125 95 110 525 71 400 28 163 276 16 59 375

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000523035
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl820,953,642 - 20,968,904 (+)Ensembl
RefSeq Acc Id: ENST00000523852
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl820,953,127 - 20,962,895 (+)Ensembl
RefSeq Acc Id: NR_130773
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38820,953,633 - 20,968,938 (+)NCBI
T2T-CHM13v2.0821,219,988 - 21,235,321 (+)NCBI
Sequence:
RefSeq Acc Id: NR_130774
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38820,953,633 - 20,968,938 (+)NCBI
T2T-CHM13v2.0821,219,988 - 21,235,321 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LINC03023 COSMIC
Ensembl Genes ENSG00000253147 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000523035 ENTREZGENE
GTEx ENSG00000253147 GTEx
HGNC ID HGNC:56154 ENTREZGENE
Human Proteome Map LINC03023 Human Proteome Map
NCBI Gene LOC102467222 ENTREZGENE
RNAcentral URS00008120F2 RNACentral
  URS0000812176 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-01-17 LINC03023  long intergenic non-protein coding RNA 3023  AC015468.1  novel transcript  Symbol and/or name change 19259463 PROVISIONAL
2020-06-25 AC015468.1  novel transcript  LOC102467222  uncharacterized LOC102467222  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LOC102467222  uncharacterized LOC102467222  AC015468.1  novel transcript  Symbol and/or name change 5135510 APPROVED