MmuINT0119688 @ mm9
Intron Retention
Gene
ENSMUSG00000030660 | Pik3c2a
Description
phosphatidylinositol 3-kinase, C2 domain containing, alpha polypeptide [Source:MGI Symbol;Acc:MGI:1203729]
Coordinates
chr7:123491634-123493656:-
Coord C1 exon
chr7:123493547-123493656
Coord A exon
chr7:123491842-123493546
Coord C2 exon
chr7:123491634-123491841
Length
1705 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGG
5' ss Score
7.37
3' ss Seq
AGTTTTTGATTATTTTGTAGGCT
3' ss Score
6.06
Exon sequences
Seq C1 exon
ATGATTCCTTCAGGATTGCCAGAACTCACAAGTATTCAGGATCTGAAATATGTTAGAGATGCACTTCAGCCCCAAACTACAGATGCTGAAGCTACTATTTTCTTTACTAG
Seq A exon
GTATGGCATGTTTAATTTTGTCAAAAAGTCCTTTGTGACAAAAAGACTAGGGATGTAGCTCAGAGGTAGAGTCCTTATCCTCTCCTCTGTAAAGTCCTGGTTGTTTATTCACCAGCAATGAAAGGAAAAGTTACTAAAAGTTGCAGCAGTGCTTAAAACAATGTTTATTCCTCTCAAAGTATATATAATCTCTGGTTTTTCAGTACATGATTTCAAATGAATGGATCTTGCTTATAAACATCTAAGAAACATGTTTTCCGCAGTAATGATAATGTGCTTCTTTTAAGGTTTTTTCTGAGATGATTTATTTTTCCAAGATTCTATCATAATAGTTTCTATGGATACCACAACCCAGCAGGAGACTGATACAGTAAGGCTGTATATTATTGCTTCACTACAGTACTTGAAGTGCATGTCAGGAAATGGCTAGCATTTGAATGCCACTGTTGCTTTCAATAAAAACAGATCTTGGCAAACATTGTTCTAAAGACTCAGTGACCATGTTCACTGAATGCTGTTGTTATGACTTCTGGGAATGGAGCTCACTTTTTTGTTCCGCGAGAGGAGGTATGAAGCACTGGCCCGCCAGATCTTTCCTAAAGTCAGGTTTGGCTGAAATGAAGGAAGCTGACTTTTCTTTTTTCTTTTTCTTCCAAAGATTTATTATATGTAAGTACACTGTAGCTGTCTTCAGAGACACCAGAAGAGGGCGTCAGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCAGGACCTTCAGAAGAGCAGTCAGTGCTCTTACCCACTGAACCATCTCTCCAGCCCCCAGAAGCTGACTTTTCAATGCTTCCCAACTTCAACCATTTTGGGTGTTTATAGTTTTTATTGTGGTTGTTCCTTTCCATTGGGGCTGGGAACCAAACCTAGGGCTGTGTACTTAGAAGCATTTTACTACAGAGCTAAATTCTGAGTCTTTTTGGTCTTGTTCTAGTCATTGGTTCCCCTAAGTGAAGCAAGTAAAGGACTACTAACTACATCTCAGCCCTGACATATATTTCTGAGTCTTCTTGTTCCTTTGGTAACCTAAATATATAATCCTAGCCTTCCTTACAAAGTGCTTCTGCAAATTCCACCATTTCAAAACTTCTTTTCCTAATTAAGTATGATCATGATTATCTAAGGGAATCTTGCCACCAAATTCTCACATGCTACTTAATAGATTTTTTAAAAATATGACTTAAAATAGCAGTCATCTTTTTTTTTTTTTGGTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACCCAGAAATTCACCTGCCTCTGCCTCCCAAGTGCTGAGGTTAAAGGCGTGCGCCACCACACCCAGCATGCTTTACTTTTTAAGACCATTTTTATTATTTCCTTTGTGTGTGGAATATGCTGCCGGCTTGTAAAGCAGGCAGATGATAATAACGTATAGGGAGTTGGTTCTCTCCTTCTACAATGCGGTCCTGGAGTTAGATCATCAGGCTTTGTGGCAAATATCCTAGCCTCCTGTGCCAACCCCATAGCCTGCTCTTAATATTTTAAAAGGAAGTGATTTTCATCTTTTATTATCTTAAGTTTAGCATATGTTCCATGAAAACTCACTATTAAAACTATTAACAAGTTTTTGATTATTTTGTAG
Seq C2 exon
GCTGATTGAGTCAAGTTTGGGAAGCATTGCCACAAAGTTTAATTTCTTCATTCATAACCTTGCTCAGCTACGTTTTTCTGGCCTTCCTTCTAATGATGAGCCCATCCTTTCATTCTCACCGAAAACATACTCCTTTAGACAAGATGGCCGGATCAAGGAAGTCTCTGTTTTCACATATCATAAGAAATACAACCCAGATAAACACTAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030660-Pik3c2a:NM_011083:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0045422=PI3_PI4_kinase=PD(4.6=27.0)
A:
NA
C2:
PF0078719=PX=PU(17.7=28.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGATTCCTTCAGGATTGCCAGA
R:
ATGTGAAAACAGAGACTTCCTTGA
Band lengths:
286-1991
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: