RnoINT0109245 @ rn6
Intron Retention
Gene
ENSRNOG00000009565 | Pdk4
Description
pyruvate dehydrogenase kinase 4 [Source:RGD Symbol;Acc:69061]
Coordinates
chr4:30552978-30553405:-
Coord C1 exon
chr4:30553221-30553405
Coord A exon
chr4:30553065-30553220
Coord C2 exon
chr4:30552978-30553064
Length
156 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TTGTTTTCATTTTGTAACAGTCC
3' ss Score
8.04
Exon sequences
Seq C1 exon
CTTTGTAGACACGCTGGTCAAAGTTCGAAACAGACATCATAATGTGGTCCCTACGATGGCACAAGGGATCCTGGAGTACAAAGACAACTGCACCGTTGACCCCGTTACCAATCAAAATCTTCAGTATTTTTTGGACCGGTTTTATATGAACCGCATTTCTACTCGGATGCTCATGAACCAGCACA
Seq A exon
GTAAGTGAGGGTCTCTTTGGACGGTGGTACAGACATGGGGACTGAACATGAGCCATGCTGAGGCTGGGCCCATGACTGGGGACTCACAGCATTTGGGGCAGTTCTAGTCAGCACCCTGAGTTTCGTAACATGTTTTTTGTTTTCATTTTGTAACAG
Seq C2 exon
TCCTCATATTCAGTGACTCAAAGACAGGAAACCCAAGCCACATTGGGAGTATCGACCCCAACTGCGATGTGGTAGCAGTAGTCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009565:ENSRNOT00000012760:4
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:
PF104364=BCDHK_Adom3=FE(37.8=100),PF0160215=Adaptin_N=PD(42.9=61.9)
A:
NA
C2:
PF104364=BCDHK_Adom3=PD(11.6=63.3)
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:
GACACGCTGGTCAAAGTTCGA
R:
CATCGCAGTTGGGGTCGATAC
Band lengths:
247-403
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]