MmuINT0117402 @ mm9
Intron Retention
Gene
ENSMUSG00000019577 | Pdk4
Description
pyruvate dehydrogenase kinase, isoenzyme 4 [Source:MGI Symbol;Acc:MGI:1351481]
Coordinates
chr6:5436678-5437174:-
Coord C1 exon
chr6:5437064-5437174
Coord A exon
chr6:5436792-5437063
Coord C2 exon
chr6:5436678-5436791
Length
272 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGG
5' ss Score
8.92
3' ss Seq
CCTTGACCTTCTACCTCCAGGCT
3' ss Score
9.24
Exon sequences
Seq C1 exon
ATTTCTGACCGAGGAGGCGGTGTTCCTCTGAGGATTACTGACCGCCTCTTTAGTTACACGTACTCCACTGCTCCAACACCTGTGATGGACAATTCCCGGAATGCCCCTTTG
Seq A exon
GTAAGGCCAATGATACAGCTCAACTTATCTCAAAACCACCTCATTGTAACGTAGGCTGAGACTTATAAAGAAGTCTTTAAGCTAGATAATAGACTTAGCTAAGTAGGCACGCAGGCCTATGAGAAATATGACCAAGCTAGCTAAGATTAGAATGAAGATCCTAAGAACTCTGACTAGGAGGAGGTATCAGTGAGGCTCCTAACGCCTTTCCATATTTGGCATTCCAGTGATCATGTTTGCATTTTCACTAACCCTTGACCTTCTACCTCCAG
Seq C2 exon
GCTGGTTTTGGTTATGGCTTGCCAATTTCTCGTCTCTACGCCAAGTATTTTCAAGGAGATCTGAATCTCTACTCTATGTCAGGTTATGGGACAGACGCTATCATCTACTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000019577-Pdk4:NM_013743:9
Average complexity
IR-S
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:
PF0251821=HATPase_c=FE(28.8=100)
A:
NA
C2:
PF0251821=HATPase_c=FE(29.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTCTGACCGAGGAGGCG
R:
AGTAGATGATAGCGTCTGTCCCA
Band lengths:
220-492
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: