PPP2R2B-IT1 (PPP2R2B intronic transcript 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: PPP2R2B-IT1 (PPP2R2B intronic transcript 1) Homo sapiens
Analyze
Symbol: PPP2R2B-IT1
Name: PPP2R2B intronic transcript 1
RGD ID: 6481071
HGNC Page HGNC:42984
Description: INTERACTS WITH propofol
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: AC008728.2
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385146,914,207 - 146,919,506 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl5146,914,207 - 146,919,506 (-)EnsemblGRCh38hg38GRCh38
GRCh375146,293,770 - 146,299,069 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5q32NCBI
HuRef5141,440,743 - 141,446,042 (-)NCBIHuRef
CHM1_15145,726,209 - 145,731,508 (-)NCBICHM1_1
T2T-CHM13v2.05147,450,274 - 147,455,574 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
propofol  (EXP)

References

Genomics


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q32(chr5:145197355-148541511)x1 copy number loss See cases [RCV000136679] Chr5:145197355..148541511 [GRCh38]
Chr5:144576918..147921074 [GRCh37]
Chr5:144557111..147901267 [NCBI36]
Chr5:5q32		 pathogenic
GRCh38/hg38 5q32(chr5:146799840-147408423)x3 copy number gain See cases [RCV000138048] Chr5:146799840..147408423 [GRCh38]
Chr5:146179403..146787986 [GRCh37]
Chr5:146159596..146768179 [NCBI36]
Chr5:5q32		 likely benign
GRCh38/hg38 5q23.3-33.2(chr5:129847794-153353546)x3 copy number gain See cases [RCV000138808] Chr5:129847794..153353546 [GRCh38]
Chr5:129183487..152733106 [GRCh37]
Chr5:129211386..152713299 [NCBI36]
Chr5:5q23.3-33.2		 pathogenic
GRCh38/hg38 5q31.3-32(chr5:141089988-149530678)x3 copy number gain See cases [RCV000139504] Chr5:141089988..149530678 [GRCh38]
Chr5:140469572..148910241 [GRCh37]
Chr5:140449756..148890434 [NCBI36]
Chr5:5q31.3-32		 pathogenic
GRCh38/hg38 5q23.3-33.2(chr5:130860928-155321811)x3 copy number gain See cases [RCV000051193] Chr5:130860928..155321811 [GRCh38]
Chr5:130196621..154701371 [GRCh37]
Chr5:130224520..154681564 [NCBI36]
Chr5:5q23.3-33.2		 pathogenic
GRCh38/hg38 5q21.3-33.2(chr5:106619588-156124387)x1 copy number loss See cases [RCV000053524] Chr5:106619588..156124387 [GRCh38]
Chr5:105955289..155551397 [GRCh37]
Chr5:105983188..155483975 [NCBI36]
Chr5:5q21.3-33.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:80
Interacting mature miRNAs:88
Transcripts:ENST00000505921
Prediction methods:Microtar, 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
High
Medium
Low 1 2 41 48 295 2 1 39
Below cutoff 99 32 71 7 10 6 301 49 917 9 76 53 1 9 278

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000505921
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl5146,914,207 - 146,919,506 (-)Ensembl
RefSeq Acc Id: NR_047115
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385146,914,207 - 146,919,506 (-)NCBI
GRCh375146,293,770 - 146,299,069 (-)NCBI
HuRef5141,440,743 - 141,446,042 (-)NCBI
CHM1_15145,726,209 - 145,731,508 (-)NCBI
T2T-CHM13v2.05147,450,274 - 147,455,574 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC PPP2R2B-IT1 COSMIC
Ensembl Genes ENSG00000249553 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000505921 ENTREZGENE
GTEx ENSG00000249553 GTEx
HGNC ID HGNC:42984 ENTREZGENE
Human Proteome Map PPP2R2B-IT1 Human Proteome Map
NCBI Gene PPP2R2B-IT1 ENTREZGENE
RNAcentral URS0000344375 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-03-03 PPP2R2B-IT1  PPP2R2B intronic transcript 1    PPP2R2B intronic transcript 1 (non-protein coding)  Symbol and/or name change 5135510 APPROVED