LNCARSR (lncRNA regulator of Akt signaling associated with HCC and RCC) - Rat Genome Database

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Gene: LNCARSR (lncRNA regulator of Akt signaling associated with HCC and RCC) Homo sapiens
Analyze
Symbol: LNCARSR
Name: lncRNA regulator of Akt signaling associated with HCC and RCC
RGD ID: 15037041
HGNC Page HGNC:53864
Description:
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: lnc-TALC
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38979,517,873 - 79,567,952 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl979,505,804 - 79,567,802 (-)EnsemblGRCh38hg38GRCh38
Cytogenetic Map9q21.31NCBI
CHM1_1982,280,093 - 82,329,999 (-)NCBICHM1_1
T2T-CHM13v2.0991,676,249 - 91,726,328 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:27117758   PMID:27886176   PMID:28464252   PMID:29555473   PMID:29678744   PMID:30391438   PMID:31038847   PMID:31053733   PMID:32558022   PMID:32798250   PMID:35637970  


Genomics

Variants

.
Variants in LNCARSR
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000148113] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445) copy number gain See cases [RCV000133791] Chr9:204193..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3 copy number gain See cases [RCV000143476] Chr9:203862..138125937 [GRCh38]
Chr9:203862..141020389 [GRCh37]
Chr9:193862..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q21.31(chr9:193412-79877816)x3 copy number gain See cases [RCV000143012] Chr9:193412..79877816 [GRCh38]
Chr9:204104..82492731 [GRCh37]
Chr9:194104..81682551 [NCBI36]
Chr9:9p24.3-q21.31		 pathogenic
GRCh38/hg38 9q21.13-21.31(chr9:73706686-80370629)x1 copy number loss See cases [RCV000052907] Chr9:73706686..80370629 [GRCh38]
Chr9:76321602..82985544 [GRCh37]
Chr9:75511422..82175364 [NCBI36]
Chr9:9q21.13-21.31		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000138962] Chr9:193412..138159073 [GRCh38]
Chr9:204104..141053525 [GRCh37]
Chr9:194104..140173346 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p24.3-q22.1(chr9:203861-88130444)x4 copy number gain See cases [RCV000141904] Chr9:203861..88130444 [GRCh38]
Chr9:203861..90745359 [GRCh37]
Chr9:193861..89935179 [NCBI36]
Chr9:9p24.3-q22.1		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124532)x3 copy number gain See cases [RCV000053745] Chr9:193412..138124532 [GRCh38]
Chr9:204193..141018984 [GRCh37]
Chr9:194193..140138805 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3 copy number gain See cases [RCV000053746] Chr9:193412..138114463 [GRCh38]
Chr9:214367..141008915 [GRCh37]
Chr9:204367..140128736 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000050348] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3 copy number gain See cases [RCV000138783] Chr9:193412..138124524 [GRCh38]
Chr9:204090..141018976 [GRCh37]
Chr9:194090..140138797 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q21.11-21.32(chr9:68499530-83670227)x1 copy number loss See cases [RCV000137963] Chr9:68499530..83670227 [GRCh38]
Chr9:71130848..86285142 [GRCh37]
Chr9:70304266..85474962 [NCBI36]
Chr9:9q21.11-21.32		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3 copy number gain See cases [RCV000141876] Chr9:203861..138125937 [GRCh38]
Chr9:203861..141020389 [GRCh37]
Chr9:193861..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q21.12-31.3(chr9:69627642-111454304)x3 copy number gain See cases [RCV000139789] Chr9:69627642..111454304 [GRCh38]
Chr9:72242558..114216584 [GRCh37]
Chr9:71432378..113256405 [NCBI36]
Chr9:9q21.12-31.3		 pathogenic
GRCh38/hg38 9q21.31-21.32(chr9:78805124-81880860)x3 copy number gain See cases [RCV000052231] Chr9:78805124..81880860 [GRCh38]
Chr9:81420040..84495775 [GRCh37]
Chr9:80609860..83685595 [NCBI36]
Chr9:9q21.31-21.32		 uncertain significance
GRCh38/hg38 9q21.11-31.2(chr9:68420430-106579493)x3 copy number gain See cases [RCV000136788] Chr9:68420430..106579493 [GRCh38]
Chr9:71130848..109341774 [GRCh37]
Chr9:70225166..108381595 [NCBI36]
Chr9:9q21.11-31.2		 pathogenic
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000139207] Chr9:193412..138159073 [GRCh38]
Chr9:68420641..141053525 [GRCh37]
Chr9:67910461..140173346 [NCBI36]
Chr9:9p11.2-q34.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:204
Count of miRNA genes:192
Interacting mature miRNAs:199
Transcripts:ENST00000413352, ENST00000424980, ENST00000608561
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
High
Medium 3
Low 3 2 3 1 25 1 2 3 9 359 2 1
Below cutoff 658 451 438 142 693 56 1075 252 1468 135 399 661 98 441 490 4

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000413352
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl979,515,643 - 79,532,342 (-)Ensembl
RefSeq Acc Id: ENST00000424980
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl979,505,804 - 79,532,342 (-)Ensembl
RefSeq Acc Id: ENST00000608561
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl979,517,953 - 79,532,321 (-)Ensembl
RefSeq Acc Id: ENST00000628133
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl979,505,858 - 79,506,999 (-)Ensembl
RefSeq Acc Id: ENST00000656806
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl979,517,873 - 79,567,767 (-)Ensembl
RefSeq Acc Id: ENST00000663687
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl979,517,865 - 79,532,336 (-)Ensembl
RefSeq Acc Id: ENST00000665514
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl979,517,873 - 79,567,777 (-)Ensembl
RefSeq Acc Id: ENST00000666862
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl979,517,878 - 79,567,773 (-)Ensembl
RefSeq Acc Id: ENST00000670754
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl979,517,811 - 79,567,802 (-)Ensembl
RefSeq Acc Id: ENST00000671232
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl979,517,873 - 79,567,759 (-)Ensembl
RefSeq Acc Id: NR_184110
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38979,517,873 - 79,567,952 (-)NCBI
T2T-CHM13v2.0991,676,249 - 91,726,328 (-)NCBI
RefSeq Acc Id: NR_184111
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38979,517,873 - 79,567,952 (-)NCBI
T2T-CHM13v2.0991,676,249 - 91,726,328 (-)NCBI
RefSeq Acc Id: NR_184112
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38979,517,873 - 79,567,952 (-)NCBI
T2T-CHM13v2.0991,676,249 - 91,726,328 (-)NCBI
RefSeq Acc Id: NR_184113
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38979,517,873 - 79,567,952 (-)NCBI
T2T-CHM13v2.0991,676,249 - 91,726,328 (-)NCBI

Additional Information

Database Acc Id Source(s)
COSMIC LNCARSR COSMIC
Ensembl Genes ENSG00000233086 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000656806 ENTREZGENE
  ENST00000665514 ENTREZGENE
  ENST00000670754 ENTREZGENE
  ENST00000671232 ENTREZGENE
GTEx ENSG00000233086 GTEx
HGNC ID HGNC:53864 ENTREZGENE
Human Proteome Map LNCARSR Human Proteome Map
NCBI Gene LNCARSR ENTREZGENE
RNAcentral URS00026A1C69 RNACentral
  URS00026A1DF2 RNACentral
  URS00026A216E RNACentral
  URS00026A271B RNACentral