RnoINT0109242 @ rn6
Intron Retention
Gene
ENSRNOG00000009565 | Pdk4
Description
pyruvate dehydrogenase kinase 4 [Source:RGD Symbol;Acc:69061]
Coordinates
chr4:30546664-30548208:-
Coord C1 exon
chr4:30548095-30548208
Coord A exon
chr4:30547007-30548094
Coord C2 exon
chr4:30546664-30547006
Length
1088 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGC
5' ss Score
9.55
3' ss Seq
TTTTCTCTACTCTCCTTTAGGCT
3' ss Score
10.62
Exon sequences
Seq C1 exon
GCTGGTTTTGGTTACGGCTTGCCGATTTCCCGTCTCTACGCCAAGTATTTTCAAGGAGATCTGAATCTCTATTCCATGTCAGGCTATGGGACAGATGCCATCATCTACTTAAAG
Seq A exon
GTATGCTTGGAACTCAGTCAAAAGCCATCTTTTCAAAGCCATGGCTTTGTTTACGCCTCTGTGCTCCATGTTCCTCTGTGAACCCTTCAAACTGAGTTAGTCTAAGGAAGCTTCCTGTTTGGGTGTGAGCACACCATCCTGTATACAGCTTACCCAAGAGGTGAGAGCTTACCTAAGCTAAGGTGTGCTACCTGTCTCAAGTGCTGACCCAGACACAGCTTAAGCTCCAGAATGAATCTTTTTCAGACAACTCCTCTTTGACCTCTGAGAGGGTAGCTAGAGCTCTCTTTTAGTCAGTCTTGTGGGTAATACATGCTAATGAAGACTCAGACTGAAACAACAAAAATCAAGACCCTTTGTAACCTTAAGACAACCCTATATAAAACCCAGGGGAAAGAAGGCTCACAAGCTGACAGTGGGGTGCCAGGCATTTCCTGTTTAAAACTGGAACTGGAGTACACAGTTTCCAGTCTCGGATAACGCCTAAATTTGTTTGTTAAGATCACCTTCCCAACTCTGTTCGTCATTTGCCAACTATTTCAAGAGAAAATGTATTTATAGCTCGTAAGAACCGCACCATCAGTCGCTTCTAGGCTTCCATTTTACTCATTGGAATTAAATGCTCACATACCCGTCACTGTCTGAAATGCTTGCTGTCCTTACTCATTTCTGAAATGAGCAAAAGTGTTCACACTGTAGGGAAAGAAGTCTGTGATAGATGAATAGTATCACCTGAAGCCTCTAATCACAGAAACACAGGTTTCTTTCTGAAAAGAACTGCCTTTCTTTTCATCTCCATTACATCAAAGGTCACCAATGGTCATGGGTAAATATTGAACACAAAATCTGTGCCCAAATTTACAATCGATCCCACACCTACAAATTAAGCTTCTATCAAATAAAGATAATAGTTTTTTAGTCATATTTTGTGAAATATCTAGAACACCATGGGTTTGGTACATTTTTTACCACAAAGTCAATTACCCGAGAGTACTTGGATATTCTATCGTACCTCTGAATGTATTGTGAATAACGGAGTACAGCCATACATCTTGTCTTAATTCGTTGTTTTCTCTACTCTCCTTTAG
Seq C2 exon
GCTTTATCATCTGAGTCTATAGAAAAACTCCCCGTCTTTAACAAGTCAGCCTTCAAACATTATCAGATGAGTTCTGAGGCTGATGACTGGTGTATCCCAAGTAAGGAACCAAAGAATCTGTCGAAGGAGAAACTGGCAGTGTGACGGGGATCTCGCCTGGCACTTTACGGGATCAAAGTGGGTCTACGGCAGTGCTGCTTCGTGAATGTGTGTGGACTCTTGTTTCCGCAAAACAAAGCAAAACAAAACCAAGCAAACGCTAGAACAGACATTGATCTGAGGAGGGACTGAGCTTGGTTATGTGACCGGGAGAAGTCAGGGCAGGGCTTCAGTAGACAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009565:ENSRNOT00000012760:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.021
Domain overlap (PFAM):
C1:
PF0251821=HATPase_c=FE(29.6=100)
A:
NA
C2:
PF0251821=HATPase_c=PD(0.8=2.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGTTTTGGTTACGGCTTGC
R:
GCGGAAACAAGAGTCCACACA
Band lengths:
342-1430
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]