DreINT0112025 @ danRer10
Intron Retention
Gene
ENSDARG00000013128 | pdk1
Description
pyruvate dehydrogenase kinase, isozyme 1 [Source:ZFIN;Acc:ZDB-GENE-091204-402]
Coordinates
chr9:3133240-3133563:-
Coord C1 exon
chr9:3133486-3133563
Coord A exon
chr9:3133317-3133485
Coord C2 exon
chr9:3133240-3133316
Length
169 bp
Sequences
Splice sites
5' ss Seq
ATGGTAACT
5' ss Score
6.06
3' ss Seq
GTGTGTGTTTTTTTCCACAGTTA
3' ss Score
11.18
Exon sequences
Seq C1 exon
ATGCTTATGAAAATGCCCGAAACCTGTGTGACCGGTATTATATGAACTCGCCCGAGCTAGTGTTGGAGGAATTTAATG
Seq A exon
GTAACTTCCTGCTGCACATTCACAAAAGGTCATAAACAGAGTTGAGAGAGAAGAGTGTCTTAATACATACTTTTAAATAAAAACGAAAGTGATGATTAAACGAGTCCGCATTACACATGGATCGATCAGAGGTGAAACTGCAGCTTTTTGTGTGTGTTTTTTTCCACAG
Seq C2 exon
TTAAAGGACCAGATAAACCCGTTACTGTGGTTTATGTACCATCTCATCTCTACCACATGGTGTTTGAGCTCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013128:ENSDART00000020861:6
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:
PF0251821=HATPase_c=PU(11.2=53.8)
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:
TGCTTATGAAAATGCCCGAAACC
R:
CTTAAAGAGCTCAAACACCATGTGG
Band lengths:
154-323
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]