RnoINT0032618 @ rn6
Intron Retention
Gene
ENSRNOG00000002841 | Cdc42bpa
Description
CDC42 binding protein kinase alpha [Source:RGD Symbol;Acc:621406]
Coordinates
chr13:98424148-98426157:+
Coord C1 exon
chr13:98424148-98424229
Coord A exon
chr13:98424230-98425940
Coord C2 exon
chr13:98425941-98426157
Length
1711 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
TGACTGTTAAATTGTTGTAGGTC
3' ss Score
7.71
Exon sequences
Seq C1 exon
AGATGAAGAATTTTCCGTGAGTTCAGTCTTGGCTTCTGATGTTATTCATGCAAGTCGAAAAGATATTCCCTGTATATTTAGA
Seq A exon
GTAAGTCTGTGAATGACTTGAACACCTACATACTTTGGGTTTTGTGCACATGCGTTTGTGTGCACATGCCCGTGAAGGCCAGATGGTGGCATCAGATATCTTCCTTGATTGCTCTCCACATTGTTTGCTGAGATGGAGTCTCACTGAGCCTGCTGCTCATAGCTGTAGTAGTTTAGCCAGCCAGCTTGCCCCAGCTGTCCCGGACTCTACCTCAGGAGCTCAAGGACAACAGACAACCCCACCTAGCTTTTACCTGGGTTCTGGGGCTCCAAGCTCTGACCCTCAGGTTTGTGCAGCGTGTGCTTTATCCACTGAGCCAACTCTCCAGCACCTAATTACTTGTTTTTAATGAGTATATTTTGCTACTCTATATAAATCATAATCCAGTATTCACATGAATACAAAATTGTGCTGAGACTTATAGAATATATCAATGTTTCTAAAGTATTCTTCATGTTCTATAATATTTTTGAGTCCCAGCTAACTTTCAAATAAATATTACCAAATGGCAGTTTCTCAAATTAAAAACAAAATTTGGTCTCTGTAAAACTTTCATTGTAAAATTGTGTTTCAGTTGTCTACTTCTTTAGAACAATATTCCAAAGCGTGAACAGTGTTCGTTGTCACTATTCTGTGCTGCTCACTGTTGCCCCTGTGCTGCATCCAGCTCGCCTGGGGCAGGAATGTGCAGAAGAATCTTTCTCTTGATCTGCAACTTTGGTGCTGCCTGGCTGTGTCAATTCTCCTCTCTCTCCCTCTTCTCTCCCCTCCTCCCTCCCTTCCTCCCTTTTCCTTTTCTTTCCTCTCCCCACCCCCCCCATAATCGCATACAAATAATTGTTAGTGGTCATTTTGGTGAGTTTAAACAGTATAAATTTATAAAACTATTCTGTTGTTACAACTCTCCTACTTCTATTTGTCTATGAATCTTACATCTAAGGAAGGTCAAAGATTAAACCTAGGCCACAGCTGTTTATTCCCCCCCTAGCTATCAAGGGAACCTGTAAAGGTTCACTTACCTGCAACTAATTTGCAGTAGAATTGTGTTGTCACTGGTGTTTAGAGCATATGTAAGTATATAAAGGGTCTCTGTAGACATGTATATGTAATATATGTGTATATTACATAAATAATAGCTTAAAAGTGCTCCGATGGACTTGTAAACTTTATTTGCATACTGTTTCTAGTATCTAGTCTTCTGTGGAAGGTCGTGAGGGGGCACGAAGACCTTCAGAGCAGTCCGATGTAATGTTTCAGAGCATTGAGACATGCTCTAGCTCTATGCCCCGGAGAGATTACTAACTTCCCCTTTATCATGGATTCTCATCTATACACTTACATTGTATCATAGTTGTTGCCTCATGAAGCTGTTAAGAGGATTAAATGAGTTAATACTTGTAAATGACTTTTCTCACTGGTACTTGATAATTTTGTGTCAGTTATTAAATTAGTATCTGTGCATTCCTGTGTATTTTGATGGCATTATGTAACACAGAGCATGAGATGATAGTAACATTTGACTTGCATCACCTCCTGCTGTTTGAATTGTAGGGTTACAGTGAGACACTTTCACTCAGTGTAACTGAAGTGTGCTACAGAGATGATTTTATAAATGCTCATTTTACTGCTGAGTGCTAAGCCAATGACCATACTCCTGAGACTAGCATAAAGATGTCTGTCTTCTCATATTGTGACTGTTAAATTGTTGTAG
Seq C2 exon
GTCACAGCCTCCCAGCTCTCAGCACCTAGTGACAAATGTTCCATCCTGATGCTAGCCGACAGCGAGACTGAGAGGAGTAAGTGGGTGGGAGTGCTGAGTGAACTCCACAAGGTTCTGAAGAAAAACAAGTTCAGAGACCGCTCAGTGTATGTCCCCAAAGAGGCTTACGACAGCACTCTACCCCTCATTAAAACAACGCAGGCCGCGGCAATCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002841:ENSRNOT00000003837:27
Average complexity
IR
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:
NO
A:
NA
C2:
PF0078017=CNH=PU(1.9=6.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAGAATTTTCCGTGAGTTCAGTCT
R:
CTATGATTGCCGCGGCCTG
Band lengths:
296-2007
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]