DreINT0112021 @ danRer10
Intron Retention
Gene
ENSDARG00000013128 | pdk1
Description
pyruvate dehydrogenase kinase, isozyme 1 [Source:ZFIN;Acc:ZDB-GENE-091204-402]
Coordinates
chr9:3140310-3140610:-
Coord C1 exon
chr9:3140469-3140610
Coord A exon
chr9:3140382-3140468
Coord C2 exon
chr9:3140310-3140381
Length
87 bp
Sequences
Splice sites
5' ss Seq
CTGGTCAGT
5' ss Score
6.6
3' ss Seq
TTTGTGTTGCGTCTCTGTAGGTA
3' ss Score
11.1
Exon sequences
Seq C1 exon
GTTCGGAGAACGCCTGTGAGAAAACGTCATTTACATTCTTAAGGCAGGAGCTGCCCGTCAGGCTGGCGAATATAATGAAAGAAATCGACTTGCTTCCTGACAACCTTCTGAGAACTCCTTCAGTGCGGCTGGTGCAGAGCTG
Seq A exon
GTCAGTCGGAATTCATGTGCGAAGTCTTATTGTTCTAATACTTGTCTGTAGATTAGCTCATTATTTGTTTGTGTTGCGTCTCTGTAG
Seq C2 exon
GTACATGCAAAGTTTTCAGGATATACTGGAATTCAAGGACAAGGATGCTGACGATGAAACAGTCAATCATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013128:ENSDART00000020861:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF104364=BCDHK_Adom3=FE(28.1=100)
A:
NA
C2:
PF104364=BCDHK_Adom3=FE(14.4=100)
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:
AACGCCTGTGAGAAAACGTCA
R:
AGCATCCTTGTCCTTGAATTCCA
Band lengths:
183-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]