LYPLAL1-AS1 (LYPLAL1 antisense RNA 1) - Rat Genome Database

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Gene: LYPLAL1-AS1 (LYPLAL1 antisense RNA 1) Homo sapiens
Analyze
Symbol: LYPLAL1-AS1
Name: LYPLAL1 antisense RNA 1
RGD ID: 13793276
HGNC Page HGNC:54054
Description: ASSOCIATED WITH Usher syndrome; INTERACTS WITH fipronil; N,N-diethyl-m-toluamide
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
GRCh381219,435,158 - 219,557,324 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1219,409,039 - 219,459,369 (-)EnsemblGRCh38hg38GRCh38
GRCh371219,608,500 - 219,730,666 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q41NCBI
HuRef1190,253,058 - 190,255,348 (-)NCBIHuRef
CHM1_11220,881,530 - 221,004,003 (-)NCBICHM1_1
T2T-CHM13v2.01218,671,437 - 218,793,577 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Usher syndrome  (IAGP)

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

Genomics

Variants

.
Variants in LYPLAL1-AS1
79 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q41(chr1:218712139-219548762)x1 copy number loss See cases [RCV000140914] Chr1:218712139..219548762 [GRCh38]
Chr1:218885481..219722104 [GRCh37]
Chr1:216952104..217788727 [NCBI36]
Chr1:1q41
uncertain significance
GRCh38/hg38 1q41(chr1:215447347-221971832)x3 copy number gain See cases [RCV000051874] Chr1:215447347..221971832 [GRCh38]
Chr1:215620690..222145174 [GRCh37]
Chr1:213687313..220211797 [NCBI36]
Chr1:1q41
pathogenic
GRCh38/hg38 1q32.3-44(chr1:214023812-248918469)x3 copy number gain See cases [RCV000050981] Chr1:214023812..248918469 [GRCh38]
Chr1:214197155..249212668 [GRCh37]
Chr1:212263778..247179291 [NCBI36]
Chr1:1q32.3-44
pathogenic
GRCh38/hg38 1q32.2-44(chr1:209963625-248918469)x3 copy number gain See cases [RCV000134979] Chr1:209963625..248918469 [GRCh38]
Chr1:210136970..249212668 [GRCh37]
Chr1:208203593..247179291 [NCBI36]
Chr1:1q32.2-44
pathogenic
GRCh38/hg38 1q32.1-42.12(chr1:204764914-225408698)x3 copy number gain See cases [RCV000142054] Chr1:204764914..225408698 [GRCh38]
Chr1:204734042..225596400 [GRCh37]
Chr1:203000665..223663023 [NCBI36]
Chr1:1q32.1-42.12
pathogenic
GRCh38/hg38 1q32.2-44(chr1:209646207-248931113)x3 copy number gain See cases [RCV000051861] Chr1:209646207..248931113 [GRCh38]
Chr1:209819552..249225312 [GRCh37]
Chr1:207886175..247191935 [NCBI36]
Chr1:1q32.2-44
pathogenic
GRCh38/hg38 1q41(chr1:216518607-219827290)x1 copy number loss See cases [RCV000053953] Chr1:216518607..219827290 [GRCh38]
Chr1:216691949..220000632 [GRCh37]
Chr1:214758572..218067255 [NCBI36]
Chr1:1q41
pathogenic
GRCh38/hg38 1q31.1-42.11(chr1:187143981-224299417)x3 copy number gain See cases [RCV000051857] Chr1:187143981..224299417 [GRCh38]
Chr1:187113113..224487119 [GRCh37]
Chr1:185379736..222553742 [NCBI36]
Chr1:1q31.1-42.11
pathogenic
GRCh38/hg38 1q41(chr1:215206760-222004068)x1 copy number loss See cases [RCV000148255] Chr1:215206760..222004068 [GRCh38]
Chr1:215380103..222177410 [GRCh37]
Chr1:213446726..220244033 [NCBI36]
Chr1:1q41
pathogenic
GRCh38/hg38 1q32.2-44(chr1:207346642-248930485)x3 copy number gain See cases [RCV000143727] Chr1:207346642..248930485 [GRCh38]
Chr1:207519987..249224684 [GRCh37]
Chr1:205586610..247191307 [NCBI36]
Chr1:1q32.2-44
pathogenic
GRCh38/hg38 1q41(chr1:215206760-222004068)x1 copy number loss See cases [RCV000050298] Chr1:215206760..222004068 [GRCh38]
Chr1:215380103..222177410 [GRCh37]
Chr1:213446726..220244033 [NCBI36]
Chr1:1q41
pathogenic
Single allele deletion Usher syndrome [RCV000505151] Chr1:216066818..222607612 [GRCh38]
Chr1:216240159..222780953 [GRCh37]
Chr1:1q41
likely pathogenic
GRCh38/hg38 1q32.2-42.13(chr1:228006998-228061271)x2 copy number loss Orofacial cleft 2 [RCV002481175] Chr1:228006998..228061271 [GRCh38]
Chr1:1q32.2-42.13
association
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:51
Interacting mature miRNAs:52
Transcripts:ENST00000441790
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 1
Medium 3 57 1 1 61
Low 153 90 128 104 76 14 1913 149 132 119 414 85 91 911 788
Below cutoff 1974 2113 1358 367 817 295 2054 1819 3090 185 906 1237 78 230 1750 2

Sequence


RefSeq Acc Id: ENST00000420762
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,435,152 - 219,442,642 (-)Ensembl
RefSeq Acc Id: ENST00000441790
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,409,523 - 219,459,194 (-)Ensembl
RefSeq Acc Id: ENST00000640010
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,435,153 - 219,459,369 (-)Ensembl
RefSeq Acc Id: ENST00000652910
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,409,538 - 219,433,081 (-)Ensembl
RefSeq Acc Id: ENST00000653604
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,409,039 - 219,433,142 (-)Ensembl
RefSeq Acc Id: ENST00000658964
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,409,538 - 219,433,030 (-)Ensembl
RefSeq Acc Id: ENST00000664470
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,409,039 - 219,433,098 (-)Ensembl
RefSeq Acc Id: ENST00000667916
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,409,041 - 219,433,096 (-)Ensembl
RefSeq Acc Id: NR_135822
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381219,435,158 - 219,557,324 (-)NCBI
T2T-CHM13v2.01218,671,437 - 218,793,577 (-)NCBI
Sequence:
Promoters
RGD ID:15095349
Promoter ID:EPDNEWNC_H180
Type:initiation region
Name:LYPLAL1-AS1_1
Description:LYPLAL1 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:54054]
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
GRCh381219,442,654 - 219,442,714EPDNEWNC
RGD ID:15095351
Promoter ID:EPDNEWNC_H181
Type:initiation region
Name:LYPLAL1-AS1_2
Description:LYPLAL1 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:54054]
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
GRCh381219,459,181 - 219,459,241EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC LYPLAL1-AS1 COSMIC
Ensembl Genes ENSG00000228536 Ensembl
GTEx ENSG00000228536 GTEx
HGNC ID HGNC:54054 ENTREZGENE
Human Proteome Map LYPLAL1-AS1 Human Proteome Map
NCBI Gene LYPLAL1-AS1 ENTREZGENE
RNAcentral URS0000A77289 RNACentral