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

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Gene: HLX-AS1 (HLX antisense RNA 1) Homo sapiens
Analyze
Symbol: HLX-AS1
Name: HLX antisense RNA 1
RGD ID: 6481390
HGNC Page HGNC:42509
Description: ASSOCIATED WITH genetic disease; Usher syndrome; INTERACTS WITH benzo[a]pyrene; O-methyleugenol; triclosan
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: RP11-295M18.5
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381220,832,763 - 220,880,140 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1220,832,763 - 220,880,140 (-)EnsemblGRCh38hg38GRCh38
GRCh371221,006,105 - 221,053,482 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map1q41NCBI
HuRef1191,680,727 - 191,728,013 (-)NCBIHuRef
CHM1_11222,278,572 - 222,325,983 (-)NCBICHM1_1
T2T-CHM13v2.01220,072,481 - 220,119,930 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:16344560   PMID:20445134   PMID:21326311  


Genomics

Variants

.
Variants in HLX-AS1
17 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical 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(chr1:220673535-223683512)x1 copy number loss See cases [RCV000135795] Chr1:220673535..223683512 [GRCh38]
Chr1:220846877..223871214 [GRCh37]
Chr1:218913500..221937837 [NCBI36]
Chr1:1q41
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(chr1:207346642-248930485)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
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
NM_021958.4(HLX):c.161T>G (p.Val54Gly) single nucleotide variant Inborn genetic diseases [RCV002707849] Chr1:220880018 [GRCh38]
Chr1:221053360 [GRCh37]
Chr1:1q41
uncertain significance
NM_021958.4(HLX):c.151C>T (p.His51Tyr) single nucleotide variant Inborn genetic diseases [RCV002787239] Chr1:220880008 [GRCh38]
Chr1:221053350 [GRCh37]
Chr1:1q41
uncertain significance
NM_021958.4(HLX):c.133T>A (p.Cys45Ser) single nucleotide variant Inborn genetic diseases [RCV002719202] Chr1:220879990 [GRCh38]
Chr1:221053332 [GRCh37]
Chr1:1q41
uncertain significance
NM_021958.4(HLX):c.58G>T (p.Ala20Ser) single nucleotide variant Inborn genetic diseases [RCV003208192] Chr1:220879915 [GRCh38]
Chr1:221053257 [GRCh37]
Chr1:1q41
uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:221
Count of miRNA genes:213
Interacting mature miRNAs:218
Transcripts:ENST00000552026
Prediction methods:Miranda, Rnahybrid, Targetscan
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 6 5 2 5
Low 1105 1304 395 82 298 50 2515 992 1001 99 419 743 34 947 1756 1
Below cutoff 750 777 676 271 484 203 1107 784 1362 164 491 496 72 202 716 1

Sequence


RefSeq Acc Id: ENST00000552026
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1220,832,763 - 220,880,140 (-)Ensembl
RefSeq Acc Id: NR_046901
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381220,832,763 - 220,880,140 (-)NCBI
HuRef1191,680,727 - 191,728,013 (-)NCBI
CHM1_11222,278,572 - 222,325,983 (-)NCBI
T2T-CHM13v2.01220,072,481 - 220,119,930 (-)NCBI
Sequence:
Promoters
RGD ID:15095350
Promoter ID:EPDNEWNC_H182
Type:initiation region
Name:HLX-AS1_1
Description:HLX antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:42509]
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
GRCh381220,880,099 - 220,880,159EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC HLX-AS1 COSMIC
Ensembl Genes ENSG00000257551 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000552026 ENTREZGENE
GTEx ENSG00000257551 GTEx
HGNC ID HGNC:42509 ENTREZGENE
Human Proteome Map HLX-AS1 Human Proteome Map
NCBI Gene HLA-AS1 ENTREZGENE
RNAcentral URS00004C2BF8 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-01-21 HLX-AS1  HLX antisense RNA 1  HLA-AS1  HLA antisense RNA 1  Symbol and/or name change 5135510 APPROVED
2012-08-21 HLA-AS1  HLA antisense RNA 1  HLA-AS1  HLA antisense RNA 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED