LYPLAL1-DT (LYPLAL1 divergent transcript) - Rat Genome Database

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Gene: LYPLAL1-DT (LYPLAL1 divergent transcript) Homo sapiens
Analyze
Symbol: LYPLAL1-DT
Name: LYPLAL1 divergent transcript
RGD ID: 8656213
HGNC Page HGNC:50560
Description: ASSOCIATED WITH Usher syndrome; INTERACTS WITH lipopolysaccharide; S-(1,2-dichlorovinyl)-L-cysteine
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: LYPLAL1 antisense RNA 1 (head to head); LYPLAL1-AS1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381219,080,973 - 219,173,788 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1218,976,672 - 219,173,961 (-)EnsemblGRCh38hg38GRCh38
GRCh371219,254,315 - 219,347,130 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361217,389,941 - 217,413,752 (-)NCBINCBI36Build 36hg18NCBI36
Celera1192,541,023 - 192,564,843 (-)NCBICelera
Cytogenetic Map1q41NCBI
HuRef1189,923,990 - 190,016,868 (-)NCBIHuRef
CHM1_11220,527,155 - 220,619,943 (-)NCBICHM1_1
T2T-CHM13v2.01218,316,969 - 218,409,758 (-)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

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
Additional References at PubMed
PMID:12477932   PMID:16344560   PMID:35508613  


Genomics

Variants

.
Variants in LYPLAL1-DT
9 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_038845.1(LYPLAL1-AS1):n.492+22331C>G single nucleotide variant Lung cancer [RCV000090518] Chr1:219127608 [GRCh38]
Chr1:219300950 [GRCh37]
Chr1:1q41
uncertain significance
NR_038845.1(LYPLAL1-AS1):n.492+22298C>G single nucleotide variant Lung cancer [RCV000090519] Chr1:219127641 [GRCh38]
Chr1:219300983 [GRCh37]
Chr1:1q41
uncertain significance
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 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 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(chr1:207346642-248930485)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 [RCV000148255] Chr1:215206760..222004068 [GRCh38]
Chr1:215380103..222177410 [GRCh37]
Chr1:213446726..220244033 [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 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
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 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(chr1:215447347-221971832)x3 copy number gain See cases [RCV000051874] Chr1:215447347..221971832 [GRCh38]
Chr1:215620690..222145174 [GRCh37]
Chr1:213687313..220211797 [NCBI36]
Chr1:1q41
pathogenic
GRCh38/hg38 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
Single allele deletion Usher syndrome [RCV000505151] Chr1:216066818..222607612 [GRCh38]
Chr1:216240159..222780953 [GRCh37]
Chr1:1q41
likely pathogenic
NC_000001.11:g.(?_218405159)_(219273649_?)del deletion Loeys-Dietz syndrome 4 [RCV001824378] Chr1:218405159..219273649 [GRCh38]
Chr1:218578501..219446991 [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:102
Count of miRNA genes:100
Interacting mature miRNAs:102
Transcripts:ENST00000441331
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 1 1 1 1 1 1 4 4
Low 1387 1635 733 96 694 68 1676 1147 2667 237 1040 726 34 336 1342 1
Below cutoff 774 945 756 337 809 222 2069 835 974 154 273 719 119 728 1122 3

Sequence


RefSeq Acc Id: ENST00000441331
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,100,626 - 219,173,748 (-)Ensembl
RefSeq Acc Id: ENST00000654859
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,047,406 - 219,173,820 (-)Ensembl
RefSeq Acc Id: ENST00000655283
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1218,990,274 - 219,173,759 (-)Ensembl
RefSeq Acc Id: ENST00000657470
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1218,989,823 - 219,173,779 (-)Ensembl
RefSeq Acc Id: ENST00000658274
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,080,970 - 219,173,768 (-)Ensembl
RefSeq Acc Id: ENST00000661230
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,028,286 - 219,173,698 (-)Ensembl
RefSeq Acc Id: ENST00000663684
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1218,983,023 - 219,173,493 (-)Ensembl
RefSeq Acc Id: ENST00000668290
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,047,472 - 219,173,961 (-)Ensembl
RefSeq Acc Id: ENST00000669535
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,048,294 - 219,173,705 (-)Ensembl
RefSeq Acc Id: ENST00000670257
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,080,969 - 219,173,798 (-)Ensembl
RefSeq Acc Id: ENST00000670576
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,048,300 - 219,173,517 (-)Ensembl
RefSeq Acc Id: ENST00000685043
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1218,984,717 - 219,173,820 (-)Ensembl
RefSeq Acc Id: ENST00000685426
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,047,405 - 219,173,779 (-)Ensembl
RefSeq Acc Id: ENST00000685878
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,048,277 - 219,173,779 (-)Ensembl
RefSeq Acc Id: ENST00000686513
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,080,971 - 219,173,798 (-)Ensembl
RefSeq Acc Id: ENST00000687117
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,080,973 - 219,173,725 (-)Ensembl
RefSeq Acc Id: ENST00000690528
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,048,280 - 219,173,761 (-)Ensembl
RefSeq Acc Id: ENST00000691001
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1218,976,672 - 219,173,768 (-)Ensembl
RefSeq Acc Id: ENST00000692527
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,105,870 - 219,173,768 (-)Ensembl
RefSeq Acc Id: ENST00000702786
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1218,984,692 - 219,173,761 (-)Ensembl
RefSeq Acc Id: ENST00000702804
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1219,049,048 - 219,173,788 (-)Ensembl
RefSeq Acc Id: NR_038845
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381219,080,973 - 219,173,788 (-)NCBI
HuRef1189,923,990 - 190,016,868 (-)NCBI
CHM1_11220,527,155 - 220,619,943 (-)NCBI
T2T-CHM13v2.01218,316,969 - 218,409,758 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC LYPLAL1-DT COSMIC
Ensembl Genes ENSG00000228063 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000670257 ENTREZGENE
GTEx ENSG00000228063 GTEx
HGNC ID HGNC:50560 ENTREZGENE
Human Proteome Map LYPLAL1-DT Human Proteome Map
NCBI Gene LYPLAL1-AS1 ENTREZGENE
RNAcentral URS000075B5F8 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-03-27 LYPLAL1-DT  LYPLAL1 divergent transcript  LYPLAL1-AS1  LYPLAL1 antisense RNA 1 (head to head)  Symbol and/or name change 5135510 APPROVED