RGPD4-AS1 (RGPD4 antisense RNA 1 (head to head)) - Rat Genome Database
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Gene: RGPD4-AS1 (RGPD4 antisense RNA 1 (head to head)) Homo sapiens
Analyze
Symbol: RGPD4-AS1
Name: RGPD4 antisense RNA 1 (head to head)
RGD ID: 7380196
HGNC Page HGNC
Description: ASSOCIATED WITH schizophrenia; INTERACTS WITH aflatoxin B1; valproic acid
Type: ncrna
RefSeq Status: VALIDATED
Also known as: AC096655.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2107,823,063 - 107,826,891 (-)EnsemblGRCh38hg38GRCh38
GRCh382107,823,064 - 107,826,769 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372108,439,520 - 108,443,225 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera2102,648,824 - 102,652,521 (-)NCBI
Cytogenetic Map2q12.3NCBI
HuRef2102,114,844 - 102,118,541 (-)NCBIHuRef
CHM1_12108,443,914 - 108,447,619 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

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


Genomics

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:609
Count of miRNA genes:455
Interacting mature miRNAs:478
Transcripts:ENST00000417284, ENST00000457647, ENST00000593452, ENST00000594764, ENST00000609354, ENST00000609972
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 330
Low 4 6 10 6 5 1 5 44 10 1 3
Below cutoff 380 311 324 111 327 93 634 234 555 136 253 416 27 128 265 4

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000417284
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,824,041 - 107,826,807 (-)Ensembl
RefSeq Acc Id: ENST00000457647
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,823,063 - 107,826,891 (-)Ensembl
RefSeq Acc Id: ENST00000593452
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,825,741 - 107,826,870 (-)Ensembl
RefSeq Acc Id: ENST00000594764
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,825,741 - 107,826,836 (-)Ensembl
RefSeq Acc Id: ENST00000609354
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,824,113 - 107,826,455 (-)Ensembl
RefSeq Acc Id: ENST00000609972
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2107,825,885 - 107,826,523 (-)Ensembl
RefSeq Acc Id: NR_024439
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382107,823,064 - 107,826,769 (-)NCBI
GRCh372108,439,520 - 108,443,225 (-)NCBI
HuRef2102,114,844 - 102,118,541 (-)NCBI
CHM1_12108,443,914 - 108,447,619 (-)NCBI
Sequence:
Promoters
RGD ID:15095470
Promoter ID:EPDNEWNC_H300
Type:initiation region
Name:RGPD4-AS1_1
Description:RGPD4 antisense RNA 1 (head to head) [Source:HGNCSymbol;Acc:HGNC:49273]
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
GRCh382107,826,829 - 107,826,889EPDNEWNC

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q11.2-13(chr2:101710825-110791418)x3 copy number gain See cases [RCV000138645] Chr2:101710825..110791418 [GRCh38]
Chr2:102327287..111548995 [GRCh37]
Chr2:101693719..111265466 [NCBI36]
Chr2:2q11.2-13
pathogenic
GRCh38/hg38 2q12.3(chr2:107822694-107860072)x3 copy number gain See cases [RCV000140135] Chr2:107822694..107860072 [GRCh38]
Chr2:108439150..108476528 [GRCh37]
Chr2:107805582..107842960 [NCBI36]
Chr2:2q12.3
benign
GRCh38/hg38 2q12.2-13(chr2:106516472-110576905)x3 copy number gain See cases [RCV000139569] Chr2:106516472..110576905 [GRCh38]
Chr2:107132928..111334482 [GRCh37]
Chr2:106499360..110857227 [NCBI36]
Chr2:2q12.2-13
uncertain significance
GRCh38/hg38 2q12.2-14.1(chr2:106428663-112379067)x3 copy number gain See cases [RCV000140834] Chr2:106428663..112379067 [GRCh38]
Chr2:107045119..113136644 [GRCh37]
Chr2:106411551..112853115 [NCBI36]
Chr2:2q12.2-14.1
uncertain significance
GRCh38/hg38 2q12.3(chr2:107822694-107825068)x3 copy number gain See cases [RCV000141059] Chr2:107822694..107825068 [GRCh38]
Chr2:108439150..108441524 [GRCh37]
Chr2:107805582..107807956 [NCBI36]
Chr2:2q12.3
benign
GRCh38/hg38 2q11.1-13(chr2:94678532-110602409)x3 copy number gain See cases [RCV000141075] Chr2:94678532..110602409 [GRCh38]
Chr2:95344257..111359986 [GRCh37]
Chr2:94707984..111076455 [NCBI36]
Chr2:2q11.1-13
pathogenic
GRCh38/hg38 2q12.2-12.3(chr2:106260759-107904531)x1 copy number loss See cases [RCV000051289] Chr2:106260759..107904531 [GRCh38]
Chr2:106877215..108520987 [GRCh37]
Chr2:106243647..107887419 [NCBI36]
Chr2:2q12.2-12.3
uncertain significance
GRCh38/hg38 2q11.2-12.3(chr2:100378510-108472871)x3 copy number gain See cases [RCV000050836] Chr2:100378510..108472871 [GRCh38]
Chr2:100994972..109089327 [GRCh37]
Chr2:100361404..108455759 [NCBI36]
Chr2:2q11.2-12.3
pathogenic
GRCh38/hg38 2q11.2-13(chr2:97672522-110211318)x3 copy number gain See cases [RCV000052947] Chr2:97672522..110211318 [GRCh38]
Chr2:98288985..110968895 [GRCh37]
Chr2:97655417..110326184 [NCBI36]
Chr2:2q11.2-13
pathogenic
GRCh38/hg38 2q12.2-12.3(chr2:105828398-108080417)x3 copy number gain See cases [RCV000052691] Chr2:105828398..108080417 [GRCh38]
Chr2:106444854..108696873 [GRCh37]
Chr2:105811286..108063305 [NCBI36]
Chr2:2q12.2-12.3
uncertain significance
GRCh38/hg38 2q12.2-13(chr2:106696282-110223328)x3 copy number gain See cases [RCV000053141] Chr2:106696282..110223328 [GRCh38]
Chr2:107312738..110980905 [GRCh37]
Chr2:106679170..110338194 [NCBI36]
Chr2:2q12.2-13
uncertain significance
NC_000002.12:g.(?_106480385)_(107825992_?)del deletion Schizophrenia [RCV000416711] Chr2:106480385..107825992 [GRCh38]
Chr2:107096841..108442448 [GRCh37]
Chr2:106463273..107808880 [NCBI36]
Chr2:2q12.2-12.3
likely pathogenic
Single allele deletion not provided [RCV000677995] Chr2:106312802..107890728 [GRCh38]
Chr2:106929257..108507183 [GRCh37]
Chr2:2q12.2-12.3
uncertain significance
NC_000002.12:g.(?_106445028)_(107839483_?)del deletion Schizophrenia [RCV000754224] Chr2:106445028..107839483 [GRCh38]
Chr2:2q12.2-12.3
likely pathogenic

Additional Information

Database Acc Id Source(s)
COSMIC RGPD4-AS1 COSMIC
Ensembl Genes ENSG00000230651 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000457647 ENTREZGENE
GTEx ENSG00000230651 GTEx
HGNC ID HGNC:49273 ENTREZGENE
Human Proteome Map RGPD4-AS1 Human Proteome Map
NCBI Gene RGPD4-AS1 ENTREZGENE
RNAcentral URS000075E4D9 RNACentral
UniGene Hs.386155 ENTREZGENE