RnoINT0111230 @ rn6
Intron Retention
Gene
ENSRNOG00000020479 | Pik3c2a
Description
phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha [Source:RGD Symbol;Acc:1310389]
Coordinates
chr1:185289449-185291423:+
Coord C1 exon
chr1:185289449-185289592
Coord A exon
chr1:185289593-185291377
Coord C2 exon
chr1:185291378-185291423
Length
1785 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
ATTGATACATGTATATACAGGTG
3' ss Score
4.82
Exon sequences
Seq C1 exon
AACCAGCACCGAGCTATTGATCAAGTGATTAAAGCAGTAAGAAAAATCTGTAGTGCTTTAGATGGGGTTGAGACCCCCGCCGTCACAGAAGCAGTGAAGAAGCTAAAGCGAGCAGTTAACCTTCCAAGGAACAAAAGTGCTGAT
Seq A exon
GTGAGTATGTGTGTGGACTTAAGTGACCACTGTCATTTACACAGGATGCTCATCTCTTTAGACAAAATATTCATTTAAAATTTTTGACTTTTACTTTTGGGTTTGTTGAATTGGTTTTTGGTAAGGTGGGGATTCCTTGTTGAAATGGTGAAAGAGCTTTGTGAACATTGACACTAAATAGTGGATTCAAATTATCTTCCTTCTAGAAGTGAGATCCCTGGCGATTTAAGAAACCTAGAGAGTAGTGCTTGCAGTCCTCCCTTGATGGAAATGCCCATGCTCATTATGGCTCATTGTGCTCATTCAAGTGGCATTGCCTTAGAAGCAGCCAGATATTGAGTCTTCTGTTATGTATGTGTCAGTTTTTAGTAAAACTATGTTCCATGATACTTCCTTCCATGGGATTTTAATAAATTCAGTTCATAGAAATGTTTATGTCTTTTATTGAAAGGAATAAAGAAAAAGTGCCTCTCATAAGCTACTGTACATTTTAAGGAGAAGCTATGTCATTGGCCTGCTCCTCTGTGTCTTCATGCTCATGGGTCTACTCATTTTTGCAGAAGTTCTAGCTGTGTAACACTTAAAGATTTAAGTGTCCTCTTCATTTTGTTTTGTTTGGTTGGGGTTTTTTGGGGGGGAGTAGGAGTTCTGTTTAAAAATTATTTGGAGGGGTTGGGGATTTAGCTCAGTGGTAGCGCAAAGCACTGGGTTCAGTCCTCAGCTCTGGGGGAATAAAAGATTATTTGGAAACTCAGTCGCCATAGATCCTAATGTCTGAAGTTTCTGCTTTTTTCATTCCTTTATTGCATAAAGAAAGAGTAAAATGTAGTCAACATGGGAGTTTACCTTTAAAATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATAAAGTTGGTAAGTTATATTTATAGTAAATTGGTATGTATATTACAGTAATTATGTCTCCAACTTACTGTACTTTTGCCAAGGAAGTTCTGAACTTCTGTCCTGCTCTTCTTACTTCATAGGTGCCGACCGCAGGCGCACACTACCATGCCAGCCTTTTGTTTCTTTCTTTTCTTTGAGTCAAGGTCTCACTCTGGCCCAGGCTGGCCTTGAACTTGATGTATTTCTCCTTCCTTAGCTTCCCAGATCTCTGAGTTCAAAGCTAATCTGGGCTACATGGTAGTAAGACCCCGTTTTAAAAAAACAAAACAAAACAAAACATAGGTTTATATTTTTCACTTTTTTCTTTGGTCATTCTGCATTTGTGTGTGTGTGCACATGTGTGCGCGTGCGTGCGCGTGCGTGTATGGATGCAGTTTTTCATGTAGGTATATGGTTATGTGTTGTGGTGGGCAAATGTCCATGTGGAGGCTGGAGGTGTACAACAGATGTTAGCTGCTCTCCTCTCCTTTTGAGACCGTACCTCTTTTACGTGGGTGCAGGGAATTCTTCCGCATGCTTTCTTGGCAGTTGTTGTATCAACTGAGGCGTTTCCATAGCCCTCCATTTCTTTGTTTGCTATTTTATTAACTTTTGAGGCATGTTTGGCAGATTTCTTCTGAGAAGGGTTTCATTGACATTTAAAGAAATGTATCAAAAGTAAAGGTTATTTAAAACAAAAGCAAAGGAGGGTGGTGATACACTCCTGTTATCCCATCATTTTGGATGAGGATCAGTTTAGCAAGTTTGAGACCAGCCTGGGCTACACAAGTCTCTCTCAAAAATGGAAGAAAAAATAAGCATTTTATATTAAATTGTGGTCGATTTCTGACTAATTGATACATGTATATACAG
Seq C2 exon
GTGACTTCATTATCTGGAGGAGATACTAGCAAGAACTCAACTAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020479:ENSRNOT00000055120:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.062 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACCGAGCTATTGATCAAGTGA
R:
CCCTAGTTGAGTTCTTGCTAGT
Band lengths:
185-1970
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]