LRRC52-AS1 (LRRC52 antisense RNA 1) - Rat Genome Database

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Gene: LRRC52-AS1 (LRRC52 antisense RNA 1) Homo sapiens
Analyze
Symbol: LRRC52-AS1
Name: LRRC52 antisense RNA 1
RGD ID: 13793331
HGNC Page HGNC:54044
Description: INTERACTS WITH aflatoxin B1; Aflatoxin B2 alpha; benzo[a]pyrene
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
GRCh381165,476,842 - 165,582,155 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1165,476,833 - 165,582,155 (-)EnsemblGRCh38hg38GRCh38
GRCh371165,446,079 - 165,551,392 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera1138,551,249 - 138,656,589 (-)NCBICelera
Cytogenetic Map1q23.3-q24.1NCBI
HuRef1136,692,840 - 136,798,188 (-)NCBIHuRef
CHM1_11166,868,792 - 166,974,047 (-)NCBICHM1_1
T2T-CHM13v2.01164,823,196 - 164,928,618 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:22903471   PMID:31855284  


Genomics

Variants

.
Variants in LRRC52-AS1
14 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q23.3-25.1(chr1:163382523-175877022)x1 copy number loss See cases [RCV000143292] Chr1:163382523..175877022 [GRCh38]
Chr1:163352313..175846158 [GRCh37]
Chr1:161618937..174112781 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q23.3-24.2(chr1:162040050-167480663)x1 copy number loss See cases [RCV000053915] Chr1:162040050..167480663 [GRCh38]
Chr1:162009840..167449900 [GRCh37]
Chr1:160276464..165716524 [NCBI36]
Chr1:1q23.3-24.2		 pathogenic
GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3 copy number gain See cases [RCV000051856] Chr1:164922655..180061589 [GRCh38]
Chr1:164891892..180030724 [GRCh37]
Chr1:163158516..178297347 [NCBI36]
Chr1:1q23.3-25.2		 pathogenic
GRCh38/hg38 1q23.3-25.1(chr1:161740907-173965154)x1 copy number loss See cases [RCV000053914] Chr1:161740907..173965154 [GRCh38]
Chr1:161710697..173934292 [GRCh37]
Chr1:159977321..172200915 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3 copy number gain See cases [RCV000051854] Chr1:157747246..176021247 [GRCh38]
Chr1:157717036..175990383 [GRCh37]
Chr1:155983660..174257006 [NCBI36]
Chr1:1q23.1-25.1		 pathogenic
GRCh38/hg38 1q23.3-24.1(chr1:164547546-165689403)x1 copy number loss See cases [RCV000053213] Chr1:164547546..165689403 [GRCh38]
Chr1:164516783..165658640 [GRCh37]
Chr1:162783407..163925264 [NCBI36]
Chr1:1q23.3-24.1		 uncertain significance
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2		 pathogenic
GRCh38/hg38 1q23.2-24.1(chr1:159479887-166895086)x1 copy number loss See cases [RCV000051172] Chr1:159479887..166895086 [GRCh38]
Chr1:159449677..166864323 [GRCh37]
Chr1:157716301..165130947 [NCBI36]
Chr1:1q23.2-24.1		 pathogenic
NM_001005214.4(LRRC52):c.345G>C (p.Ser115=) single nucleotide variant not provided [RCV000886945] Chr1:165544641 [GRCh38]
Chr1:165513878 [GRCh37]
Chr1:1q24.1		 benign
NM_001005214.4(LRRC52):c.829C>T (p.Arg277Cys) single nucleotide variant not provided [RCV000964487] Chr1:165563711 [GRCh38]
Chr1:165532948 [GRCh37]
Chr1:1q24.1		 benign
NM_001005214.4(LRRC52):c.772G>A (p.Ala258Thr) single nucleotide variant not specified [RCV004184993] Chr1:165563654 [GRCh38]
Chr1:165532891 [GRCh37]
Chr1:1q24.1		 uncertain significance
NM_001005214.4(LRRC52):c.269G>A (p.Arg90Gln) single nucleotide variant not specified [RCV004245364] Chr1:165544565 [GRCh38]
Chr1:165513802 [GRCh37]
Chr1:1q24.1		 likely benign
NM_001005214.4(LRRC52):c.889C>T (p.Arg297Trp) single nucleotide variant not specified [RCV004170976] Chr1:165563771 [GRCh38]
Chr1:165533008 [GRCh37]
Chr1:1q24.1		 uncertain significance
NM_001005214.4(LRRC52):c.136G>A (p.Glu46Lys) single nucleotide variant not specified [RCV004071126] Chr1:165544432 [GRCh38]
Chr1:165513669 [GRCh37]
Chr1:1q24.1		 uncertain significance
NM_001005214.4(LRRC52):c.914C>T (p.Ser305Leu) single nucleotide variant not specified [RCV004195730] Chr1:165563796 [GRCh38]
Chr1:165533033 [GRCh37]
Chr1:1q24.1		 uncertain significance
NM_001005214.4(LRRC52):c.773C>T (p.Ala258Val) single nucleotide variant not specified [RCV004275152] Chr1:165563655 [GRCh38]
Chr1:165532892 [GRCh37]
Chr1:1q24.1		 uncertain significance
NM_001005214.4(LRRC52):c.7C>A (p.Leu3Ile) single nucleotide variant not specified [RCV004320061] Chr1:165544303 [GRCh38]
Chr1:165513540 [GRCh37]
Chr1:1q24.1		 uncertain significance
NM_001005214.4(LRRC52):c.11C>T (p.Ala4Val) single nucleotide variant not specified [RCV004290989] Chr1:165544307 [GRCh38]
Chr1:165513544 [GRCh37]
Chr1:1q24.1		 uncertain significance
NM_001005214.4(LRRC52):c.698G>A (p.Arg233Gln) single nucleotide variant not specified [RCV004350196] Chr1:165563580 [GRCh38]
Chr1:165532817 [GRCh37]
Chr1:1q24.1		 uncertain significance
NM_001005214.4(LRRC52):c.316C>T (p.Leu106Phe) single nucleotide variant not specified [RCV004415682] Chr1:165544612 [GRCh38]
Chr1:165513849 [GRCh37]
Chr1:1q24.1		 uncertain significance
NM_001005214.4(LRRC52):c.62T>G (p.Val21Gly) single nucleotide variant not specified [RCV004415683] Chr1:165544358 [GRCh38]
Chr1:165513595 [GRCh37]
Chr1:1q24.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1047
Count of miRNA genes:596
Interacting mature miRNAs:644
Transcripts:ENST00000415000, ENST00000416424, ENST00000418925, ENST00000421273, ENST00000438275, ENST00000452283, ENST00000454251
Prediction methods:Microtar, 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 1 6 139 6
Low 12 122 129 2 102 2 67 155 22 26 254 153 1 63
Below cutoff 1073 951 855 79 375 36 1419 1252 1512 145 240 1055 43 276 1075 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000415000
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,833 - 165,527,795 (-)Ensembl
RefSeq Acc Id: ENST00000416424
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,841 - 165,582,155 (-)Ensembl
RefSeq Acc Id: ENST00000418925
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,493,073 - 165,501,670 (-)Ensembl
RefSeq Acc Id: ENST00000421273
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,842 - 165,582,104 (-)Ensembl
RefSeq Acc Id: ENST00000438275
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,489,575 - 165,582,128 (-)Ensembl
RefSeq Acc Id: ENST00000452283
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,492,961 - 165,539,612 (-)Ensembl
RefSeq Acc Id: ENST00000454251
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,525,165 - 165,528,884 (-)Ensembl
RefSeq Acc Id: ENST00000656941
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,838 - 165,543,758 (-)Ensembl
RefSeq Acc Id: ENST00000658987
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,841 - 165,546,873 (-)Ensembl
RefSeq Acc Id: ENST00000665666
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,841 - 165,582,092 (-)Ensembl
RefSeq Acc Id: ENST00000666433
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,489,575 - 165,527,673 (-)Ensembl
RefSeq Acc Id: ENST00000685058
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,833 - 165,527,786 (-)Ensembl
RefSeq Acc Id: ENST00000685245
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,839 - 165,527,795 (-)Ensembl
RefSeq Acc Id: ENST00000688379
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,489,575 - 165,527,761 (-)Ensembl
RefSeq Acc Id: ENST00000690583
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,833 - 165,527,794 (-)Ensembl
RefSeq Acc Id: ENST00000690611
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,839 - 165,527,670 (-)Ensembl
RefSeq Acc Id: ENST00000690955
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,476,837 - 165,527,670 (-)Ensembl
RefSeq Acc Id: ENST00000692705
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,489,575 - 165,527,795 (-)Ensembl
RefSeq Acc Id: NR_026744
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381165,476,842 - 165,582,155 (-)NCBI
T2T-CHM13v2.01164,823,196 - 164,928,618 (-)NCBI
Sequence:
Promoters
RGD ID:15095307
Promoter ID:EPDNEWNC_H135
Type:initiation region
Name:LRRC52-AS1_1
Description:LRRC52 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:54044]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381165,527,673 - 165,527,733EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LRRC52-AS1 COSMIC
Ensembl Genes ENSG00000237463 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000421273 ENTREZGENE
GTEx ENSG00000237463 GTEx
HGNC ID HGNC:54044 ENTREZGENE
Human Proteome Map LRRC52-AS1 Human Proteome Map
NCBI Gene LRRC52-AS1 ENTREZGENE
RNAcentral URS00008E3971 RNACentral