LL22NC03-63E9.3 (uncharacterized LOC648691) - Rat Genome Database

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Gene: LL22NC03-63E9.3 (uncharacterized LOC648691) Homo sapiens
Analyze
Symbol: LL22NC03-63E9.3
Name: uncharacterized LOC648691
RGD ID: 16552464
Description: INVOLVED IN miRNA-mediated post-transcriptional gene silencing (inferred); INTERACTS WITH aflatoxin B1; benzo[a]pyrene; rifampicin
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC246793.1; novel transcript, antisense to PRAME
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382222,559,343 - 22,566,599 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2222,559,343 - 22,566,602 (+)EnsemblGRCh38hg38GRCh38
GRCh372222,901,750 - 22,909,004 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map22q11.22NCBI
HuRef225,871,858 - 5,879,112 (+)NCBIHuRef
CHM1_12222,913,819 - 22,921,072 (+)NCBICHM1_1
T2T-CHM13v2.02222,982,203 - 22,989,459 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

References
Additional References at PubMed
PMID:12477932  


Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 22q11.21-11.22(chr22:21151069-22562663)x1 copy number loss See cases [RCV000051017] Chr22:21151069..22562663 [GRCh38]
Chr22:21505358..22905068 [GRCh37]
Chr22:19835358..21235068 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21454661-24247140)x1 copy number loss See cases [RCV000137685] Chr22:21454661..24247140 [GRCh38]
Chr22:21808950..24643108 [GRCh37]
Chr22:20138950..22973108 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.22(chr22:22374043-22886630)x1 copy number loss See cases [RCV000135086] Chr22:22374043..22886630 [GRCh38]
Chr22:22728411..23228810 [GRCh37]
Chr22:21058411..21558810 [NCBI36]
Chr22:22q11.22		 benign
GRCh38/hg38 22q11.21-11.23(chr22:21443815-23397298)x1 copy number loss See cases [RCV000053075] Chr22:21443815..23397298 [GRCh38]
Chr22:21798104..23739485 [GRCh37]
Chr22:20128104..22069485 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21454661-22562663)x1 copy number loss See cases [RCV000053082] Chr22:21454661..22562663 [GRCh38]
Chr22:21808950..22905068 [GRCh37]
Chr22:20138950..21235068 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic|likely pathogenic|conflicting interpretations of pathogenicity|conflicting data from submitters
GRCh38/hg38 22q11.21-11.23(chr22:21562911-24307688)x1 copy number loss See cases [RCV000053090] Chr22:21562911..24307688 [GRCh38]
Chr22:21917200..24703656 [GRCh37]
Chr22:20247200..23033656 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.1-11.23(chr22:16916608-24358936)x3 copy number gain See cases [RCV000053104] Chr22:16916608..24358936 [GRCh38]
Chr22:17397498..24754904 [GRCh37]
Chr22:15777498..23084904 [NCBI36]
Chr22:22q11.1-11.23		 pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21386914-23305976)x3 copy number gain See cases [RCV000053158] Chr22:21386914..23305976 [GRCh38]
Chr22:21741203..23648163 [GRCh37]
Chr22:20071203..21978163 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic|uncertain significance
GRCh38/hg38 22q11.21-11.22(chr22:21454649-22562620)x1 copy number loss See cases [RCV000136017] Chr22:21454649..22562620 [GRCh38]
Chr22:21808938..22905025 [GRCh37]
Chr22:20138938..21235025 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21151097-22562620)x1 copy number loss See cases [RCV000139333] Chr22:21151097..22562620 [GRCh38]
Chr22:21505386..22905025 [GRCh37]
Chr22:19835386..21235025 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21454661-23414686)x1 copy number loss See cases [RCV000135739] Chr22:21454661..23414686 [GRCh38]
Chr22:21808950..23756873 [GRCh37]
Chr22:20138950..22086873 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.21-12.3(chr22:18178957-31821193)x3 copy number gain See cases [RCV000050768] Chr22:18178957..31821193 [GRCh38]
Chr22:18661724..32217179 [GRCh37]
Chr22:17041724..30547179 [NCBI36]
Chr22:22q11.21-12.3		 pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21443815-24235645)x1 copy number loss See cases [RCV000053074] Chr22:21443815..24235645 [GRCh38]
Chr22:21798104..24631613 [GRCh37]
Chr22:20128104..22961613 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21623411-22617259)x1 copy number loss See cases [RCV000053107] Chr22:21623411..22617259 [GRCh38]
Chr22:21977700..22959729 [GRCh37]
Chr22:20307700..21289729 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21447344-22655838)x1 copy number loss See cases [RCV000141561] Chr22:21447344..22655838 [GRCh38]
Chr22:21801633..22998308 [GRCh37]
Chr22:20131633..21328308 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21444416-22574173)x1 copy number loss See cases [RCV000136776] Chr22:21444416..22574173 [GRCh38]
Chr22:21798705..22916612 [GRCh37]
Chr22:20128705..21246612 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21454661-22617194)x1 copy number loss See cases [RCV000143267] Chr22:21454661..22617194 [GRCh38]
Chr22:21808950..22959664 [GRCh37]
Chr22:20138950..21289664 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic|uncertain significance|conflicting data from submitters
GRCh38/hg38 22q11.21-12.3(chr22:20907226-37187347)x3 copy number gain See cases [RCV000137926] Chr22:20907226..37187347 [GRCh38]
Chr22:21261514..37583387 [GRCh37]
Chr22:19591514..35913333 [NCBI36]
Chr22:22q11.21-12.3		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21454649-22562620)x3 copy number gain See cases [RCV000136016] Chr22:21454649..22562620 [GRCh38]
Chr22:21808938..22905025 [GRCh37]
Chr22:20138938..21235025 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic|uncertain significance
GRCh38/hg38 22q11.21-11.22(chr22:21583391-22647760)x3 copy number gain See cases [RCV000140091] Chr22:21583391..22647760 [GRCh38]
Chr22:21937680..22990230 [GRCh37]
Chr22:20267680..21320230 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21151069-22617194)x3 copy number gain See cases [RCV000137493] Chr22:21151069..22617194 [GRCh38]
Chr22:21505358..22959664 [GRCh37]
Chr22:19835358..21289664 [NCBI36]
Chr22:22q11.21-11.22		 uncertain significance
GRCh38/hg38 22q11.21-11.23(chr22:21454661-23312035)x1 copy number loss See cases [RCV000137767] Chr22:21454661..23312035 [GRCh38]
Chr22:21808950..23654222 [GRCh37]
Chr22:20138950..21984222 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21454461-24247296)x1 copy number loss See cases [RCV000053077] Chr22:21454461..24247296 [GRCh38]
Chr22:21808750..24643264 [GRCh37]
Chr22:20138750..22973264 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21454661-23414686)x3 copy number gain See cases [RCV000053159] Chr22:21454661..23414686 [GRCh38]
Chr22:21808950..23756873 [GRCh37]
Chr22:20138950..22086873 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic|uncertain significance|conflicting data from submitters
GRCh38/hg38 22q11.21-11.22(chr22:21623411-22651271)x3 copy number gain See cases [RCV000053160] Chr22:21623411..22651271 [GRCh38]
Chr22:21977700..22993741 [GRCh37]
Chr22:20307700..21323741 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic|uncertain significance
GRCh38/hg38 22q11.21-11.23(chr22:20726972-24197852)x1 copy number loss See cases [RCV000136889] Chr22:20726972..24197852 [GRCh38]
Chr22:21081260..24593820 [GRCh37]
Chr22:19411260..22923820 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21151069-22617194)x1 copy number loss See cases [RCV000137494] Chr22:21151069..22617194 [GRCh38]
Chr22:21505358..22959664 [GRCh37]
Chr22:19835358..21289664 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:18178932-22562620)x3 copy number gain See cases [RCV000139316] Chr22:18178932..22562620 [GRCh38]
Chr22:18661699..22905025 [GRCh37]
Chr22:17041699..21235025 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21457690-24220231)x1 copy number loss See cases [RCV000053087] Chr22:21457690..24220231 [GRCh38]
Chr22:21811979..24616199 [GRCh37]
Chr22:20141979..22946199 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21623411-23315617)x1 copy number loss See cases [RCV000053108] Chr22:21623411..23315617 [GRCh38]
Chr22:21977700..23657804 [GRCh37]
Chr22:20307700..21987804 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21207181-24247140)x3 copy number gain See cases [RCV000138673] Chr22:21207181..24247140 [GRCh38]
Chr22:21561470..24643108 [GRCh37]
Chr22:19891470..22973108 [NCBI36]
Chr22:22q11.21-11.23		 uncertain significance
GRCh38/hg38 22q11.21-11.23(chr22:18339130-23480799)x1 copy number loss See cases [RCV000141233] Chr22:18339130..23480799 [GRCh38]
Chr22:20279766..23822986 [GRCh37]
Chr22:18659766..22152986 [NCBI36]
Chr22:22q11.21-11.23		 pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916743-50739785)x3 copy number gain See cases [RCV000134730] Chr22:16916743..50739785 [GRCh38]
Chr22:17397633..51178213 [GRCh37]
Chr22:15777633..49525079 [NCBI36]
Chr22:22q11.1-13.33		 pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21603122-22562663)x1 copy number loss See cases [RCV000051147] Chr22:21603122..22562663 [GRCh38]
Chr22:21957411..22905068 [GRCh37]
Chr22:20287411..21235068 [NCBI36]
Chr22:22q11.21-11.22		 pathogenic
GRCh38/hg38 22q11.1-13.33(chr22:16916608-50739836)x3 copy number gain See cases [RCV000133646] Chr22:16916608..50739836 [GRCh38]
Chr22:17397498..51178264 [GRCh37]
Chr22:15777498..49525130 [NCBI36]
Chr22:22q11.1-13.33		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1312
Count of miRNA genes:829
Interacting mature miRNAs:955
Transcripts:ENST00000407120
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

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
131 695 321 250 1034 496 747 206 665 75 388 1675 1243 32 621 248 857 607 135

Sequence


Ensembl Acc Id: ENST00000407120
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2222,559,343 - 22,566,602 (+)Ensembl
RefSeq Acc Id: NR_027426
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382222,559,343 - 22,566,599 (+)NCBI
T2T-CHM13v2.02222,982,203 - 22,989,459 (+)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LL22NC03-63E9.3 COSMIC
Ensembl Genes ENSG00000220891 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000407120 ENTREZGENE
GTEx ENSG00000220891 GTEx
Human Proteome Map LL22NC03-63E9.3 Human Proteome Map
NCBI Gene LL22NC03-63E9.3 ENTREZGENE
RNAcentral URS000075B2D3 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-08-20 LL22NC03-63E9.3  uncharacterized LOC648691  AC246793.1  novel transcript, antisense to PRAME  Symbol and/or name change 19259462 PROVISIONAL
2020-06-25 AC246793.1  novel transcript, antisense to PRAME  LL22NC03-63E9.3  uncharacterized LOC648691  Symbol and/or name change 19259462 PROVISIONAL
2020-06-18 LL22NC03-63E9.3  uncharacterized LOC648691  AC246793.1  novel transcript, antisense to PRAME  Symbol and/or name change 5135510 APPROVED