ATP13A4-AS1 (ATP13A4 antisense RNA 1) - Rat Genome Database

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Gene: ATP13A4-AS1 (ATP13A4 antisense RNA 1) Homo sapiens
Analyze
Symbol: ATP13A4-AS1
Name: ATP13A4 antisense RNA 1
RGD ID: 6481170
HGNC Page HGNC:41095
Description: ASSOCIATED WITH Schizophrenia; schizophrenia
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
GRCh383193,553,213 - 193,555,584 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3193,553,213 - 193,555,088 (+)EnsemblGRCh38hg38GRCh38
GRCh373193,271,002 - 193,273,373 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map3q29NCBI
HuRef3190,645,038 - 190,660,616 (+)NCBIHuRef
CHM1_13193,220,675 - 193,236,254 (+)NCBICHM1_1
T2T-CHM13v2.03196,248,538 - 196,250,903 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
schizophrenia  (IAGP)

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Schizophrenia  (IAGP)
References
Additional References at PubMed
PMID:16344560  


Genomics

Variants

.
Variants in ATP13A4-AS1
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q26.2-29(chr3:168167568-198110178)x3 copy number gain See cases [RCV000137106] Chr3:168167568..198110178 [GRCh38]
Chr3:167885356..197837049 [GRCh37]
Chr3:169368050..199321446 [NCBI36]
Chr3:3q26.2-29		 pathogenic
GRCh38/hg38 3q26.32-29(chr3:176439911-198118383)x3 copy number gain See cases [RCV000138009] Chr3:176439911..198118383 [GRCh38]
Chr3:176157699..197845254 [GRCh37]
Chr3:177640393..199329651 [NCBI36]
Chr3:3q26.32-29		 pathogenic|likely benign
GRCh38/hg38 3q29(chr3:192752937-198118383)x3 copy number gain See cases [RCV000137827] Chr3:192752937..198118383 [GRCh38]
Chr3:192470726..197845254 [GRCh37]
Chr3:193953420..199329651 [NCBI36]
Chr3:3q29		 pathogenic
GRCh38/hg38 3q27.3-29(chr3:186765148-194409416)x1 copy number loss See cases [RCV000137962] Chr3:186765148..194409416 [GRCh38]
Chr3:186482937..194130145 [GRCh37]
Chr3:187965631..195611434 [NCBI36]
Chr3:3q27.3-29		 pathogenic|likely benign
GRCh38/hg38 3q26.32-29(chr3:176168525-198118383)x3 copy number gain See cases [RCV000138662] Chr3:176168525..198118383 [GRCh38]
Chr3:175886313..197845254 [GRCh37]
Chr3:177369007..199329651 [NCBI36]
Chr3:3q26.32-29		 pathogenic
GRCh38/hg38 3q25.1-29(chr3:152100512-198118383)x3 copy number gain See cases [RCV000139435] Chr3:152100512..198118383 [GRCh38]
Chr3:151818301..197845254 [GRCh37]
Chr3:153300991..199329651 [NCBI36]
Chr3:3q25.1-29		 pathogenic
GRCh38/hg38 3q25.31-29(chr3:156321878-198113452)x3 copy number gain See cases [RCV000140849] Chr3:156321878..198113452 [GRCh38]
Chr3:156039667..197840323 [GRCh37]
Chr3:157522361..199324720 [NCBI36]
Chr3:3q25.31-29		 pathogenic
GRCh38/hg38 3q25.31-29(chr3:156118441-198125115)x3 copy number gain See cases [RCV000142310] Chr3:156118441..198125115 [GRCh38]
Chr3:155836230..197851986 [GRCh37]
Chr3:157318924..199336383 [NCBI36]
Chr3:3q25.31-29		 pathogenic
GRCh38/hg38 3q26.1-29(chr3:166137209-198125115)x3 copy number gain See cases [RCV000143694] Chr3:166137209..198125115 [GRCh38]
Chr3:165854997..197851986 [GRCh37]
Chr3:167337691..199336383 [NCBI36]
Chr3:3q26.1-29		 pathogenic
GRCh38/hg38 3q26.32-29(chr3:178411707-198110319)x3 copy number gain See cases [RCV000051736] Chr3:178411707..198110319 [GRCh38]
Chr3:178129495..197837190 [GRCh37]
Chr3:179612189..199321587 [NCBI36]
Chr3:3q26.32-29		 pathogenic
GRCh38/hg38 3q27.2-29(chr3:185920880-198110319)x3 copy number gain See cases [RCV000051738] Chr3:185920880..198110319 [GRCh38]
Chr3:185638668..197837190 [GRCh37]
Chr3:187121362..199321587 [NCBI36]
Chr3:3q27.2-29		 pathogenic
GRCh38/hg38 3q27.2-29(chr3:185485849-198110178)x1 copy number loss See cases [RCV000051608] Chr3:185485849..198110178 [GRCh38]
Chr3:185203637..197837049 [GRCh37]
Chr3:186686331..199321446 [NCBI36]
Chr3:3q27.2-29		 pathogenic
GRCh38/hg38 3q27.3-29(chr3:187446231-195029133)x1 copy number loss See cases [RCV000051610] Chr3:187446231..195029133 [GRCh38]
Chr3:187164019..194749862 [GRCh37]
Chr3:188646713..196231151 [NCBI36]
Chr3:3q27.3-29		 pathogenic
GRCh38/hg38 3q28-29(chr3:189265371-198110178)x3 copy number gain See cases [RCV000051739] Chr3:189265371..198110178 [GRCh38]
Chr3:188983160..197837049 [GRCh37]
Chr3:190465854..199321446 [NCBI36]
Chr3:3q28-29		 pathogenic
GRCh38/hg38 3q28-29(chr3:190667663-198110178)x3 copy number gain See cases [RCV000051740] Chr3:190667663..198110178 [GRCh38]
Chr3:190385452..197837049 [GRCh37]
Chr3:191868146..199321446 [NCBI36]
Chr3:3q28-29		 pathogenic
GRCh38/hg38 3q22.3-29(chr3:137126982-198110178)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|See cases [RCV000051723] Chr3:137126982..198110178 [GRCh38]
Chr3:136845824..197837049 [GRCh37]
Chr3:138328514..199321446 [NCBI36]
Chr3:3q22.3-29		 pathogenic
GRCh38/hg38 3q24-29(chr3:147521892-198096565)x3 copy number gain See cases [RCV000051725] Chr3:147521892..198096565 [GRCh38]
Chr3:147239679..197823436 [GRCh37]
Chr3:148722369..199307833 [NCBI36]
Chr3:3q24-29		 pathogenic
GRCh38/hg38 3q25.31-29(chr3:157293378-198134727)x3 copy number gain See cases [RCV000051726] Chr3:157293378..198134727 [GRCh38]
Chr3:157011167..197861598 [GRCh37]
Chr3:158493861..199345995 [NCBI36]
Chr3:3q25.31-29		 pathogenic
NC_000003.12:g.(?_187222939)_(194312782_?)del deletion Schizophrenia [RCV000754274] Chr3:187222939..194312782 [GRCh38]
Chr3:3q27.3-29		 likely pathogenic
NM_032279.4(ATP13A4):c.12T>A (p.Phe4Leu) single nucleotide variant not specified [RCV004079383] Chr3:193554788 [GRCh38]
Chr3:193272577 [GRCh37]
Chr3:3q29		 uncertain significance
NM_032279.4(ATP13A4):c.28G>A (p.Ala10Thr) single nucleotide variant not specified [RCV004193465] Chr3:193554772 [GRCh38]
Chr3:193272561 [GRCh37]
Chr3:3q29		 uncertain significance
NM_032279.4(ATP13A4):c.27C>T (p.His9=) single nucleotide variant ATP13A4-related condition [RCV003964076] Chr3:193554773 [GRCh38]
Chr3:193272562 [GRCh37]
Chr3:3q29		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:460
Count of miRNA genes:377
Interacting mature miRNAs:402
Transcripts:ENST00000426459, ENST00000431512
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
High
Medium 70
Low 33 1 330 3 10 2 44 27 353 1 4 721 1 32
Below cutoff 317 115 483 119 219 37 896 232 1980 19 234 479 83 57 582

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000426459
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3193,553,412 - 193,554,912 (+)Ensembl
RefSeq Acc Id: ENST00000431512
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3193,553,213 - 193,555,088 (+)Ensembl
RefSeq Acc Id: NR_046726
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383193,553,412 - 193,555,584 (+)NCBI
CHM1_13193,234,080 - 193,236,252 (+)NCBI
T2T-CHM13v2.03196,248,737 - 196,250,903 (+)NCBI
Sequence:
RefSeq Acc Id: NR_121666
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383193,553,213 - 193,555,584 (+)NCBI
CHM1_13193,233,881 - 193,236,252 (+)NCBI
T2T-CHM13v2.03196,248,538 - 196,250,903 (+)NCBI
Sequence:
Promoters
RGD ID:15095711
Promoter ID:EPDNEWNC_H553
Type:initiation region
Name:ATP13A4-AS1_1
Description:ATP13A4 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:41095]
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
GRCh383193,553,182 - 193,553,242EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC ATP13A4-AS1 COSMIC
Ensembl Genes ENSG00000225473 Ensembl
GTEx ENSG00000225473 GTEx
HGNC ID HGNC:41095 ENTREZGENE
Human Proteome Map ATP13A4-AS1 Human Proteome Map
NCBI Gene ATP13A4-AS1 ENTREZGENE
RNAcentral URS000075C044 RNACentral
  URS000075F0E4 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-21 ATP13A4-AS1  ATP13A4 antisense RNA 1  ATP13A4-AS1  ATP13A4 antisense RNA 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED