DreINT0112032 @ danRer10
Intron Retention
Gene
ENSDARG00000020876 | pdk2a
Description
pyruvate dehydrogenase kinase, isozyme 2a [Source:ZFIN;Acc:ZDB-GENE-120910-1]
Coordinates
chr12:28453342-28453839:-
Coord C1 exon
chr12:28453768-28453839
Coord A exon
chr12:28453527-28453767
Coord C2 exon
chr12:28453342-28453526
Length
241 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
ACACTTCATTGTGCACACAGGTT
3' ss Score
7.06
Exon sequences
Seq C1 exon
GTATATTCAGAGTTTGATGGAGATCTTGGAATTCTTGGAGAAAAGTCCAGATGACCACAGTATATTAGAAGA
Seq A exon
GTAAGTAGGAACATAAATAGTACATTTTATGAAGAAAATCTAAATGTTAGATATTGTATTTTTCACTCAGTTTAGAACCCATATTTTTTGCATTGTTTTACTTGTTTATGTTATTACGTTTAGAACTAAAAGGTATAAATTTAAATGAAAGCAATCTAACTTTTTTACATGTATTTTTCAATTTCATGTTAAATATGACATATTTCATTGCATATTTTCACACACTTCATTGTGCACACAG
Seq C2 exon
GTTTGTCGCTGCTCTGGTCAACATCCGCAACAGACACAATGATGTTGTACCCACCATGGCCCAGGGCGTGATTGAATACAAAGAGGTATTTGGTCAAGATCCAGTCACTAATCAGAATATCCAGTATTTCCTGGACCGTTTCTATTTGAGCCGGATATCCATCCGAATGCTAATCAACCAGCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020876:ENSDART00000008010:3
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(14.5=100)
A:
NA
C2:
PF104364=BCDHK_Adom3=FE(37.6=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:
TATTCAGAGTTTGATGGAGATCTTGG
R:
TGCTGGTTGATTAGCATTCGGA
Band lengths:
252-493
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]