MmuINT0117396 @ mm10
Intron Retention
Gene
ENSMUSG00000019577 | Pdk4
Description
pyruvate dehydrogenase kinase, isoenzyme 4 [Source:MGI Symbol;Acc:MGI:1351481]
Coordinates
chr6:5491830-5492777:-
Coord C1 exon
chr6:5492706-5492777
Coord A exon
chr6:5492015-5492705
Coord C2 exon
chr6:5491830-5492014
Length
691 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
ACTATGAATGTCTGGCTTAGGTT
3' ss Score
6.04
Exon sequences
Seq C1 exon
GTATATCCAGAGCCTGATGGATTTGGTGGAGTTCCATGAGAAGAGCCCAGAAGACCAGAAAGCCCTGTCAGA
Seq A exon
GTAAGTTTTCTTCTCGCAAATACATGCTTAGAAATCTGGATTCTTCTGCACACGTCTCCCAGATCTTTTTTTGAAGCTTACAGAGCTGTAGCCTCTAAATTGCTACCCCTTATAAACTAGAAGTGGAGAAATGGAGGGCTGGAATGAATGCCCGGAGTGAGCCAATGCAGAGAACTTGGAGTTTTGCTTCCCAATGAATGTCAGGCTTACTTTAAATTTAGTCCAAAGATTATATTTGCAAGGGAGTTTGCCATAACATAATTTTAATGGACTCCTGGGTCATTAGTGATTGCATACTTCTTTCCCATGTGACAATTTCTATCTAGCTAAATAGCAATCTTTAAAAAAACAAAAAACAAAAAAAAACCTGTGGTTATTTTCCACAGTGGCTTGCTAGAATCATCTTTGATTTTCAATAGTCTTTAACAAGCAGACTTAATGAACATTTTTGATAAAGGCAGCAGTCATAGCGTGAGTGGAAATACAAACCCTTCCATGAAGCTGCCTCTTCTGCTACTGTAGAAGAACGTGAGTAGAGTGCGAGTCCAAAAGAAGTTTCACCCAGAATTTTGTAATTGACTGTGCTTAGGTTGGTCCTGCAAAAAGAGCTTTAGTTTTCTCTGAAGTAACATAAGCAACAGACATTTGGGAAACTTCTTTAATGTGCACTAACTATGAATGTCTGGCTTAG
Seq C2 exon
GTTTGTAGACACGCTGGTCAAAGTTCGAAACAGACATCATAATGTGGTCCCTACAATGGCTCAAGGCATCCTGGAGTATAAAGACACCTGCACAGTGGACCCCGTTACCAATCAAAATCTTCAGTATTTTTTAGACCGGTTTTACATGAACCGCATTTCTACTCGGATGCTCATGAATCAGCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000019577:ENSMUST00000019721:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF104364=BCDHK_Adom3=PU(18.0=94.7)
A:
NA
C2:
PF104364=BCDHK_Adom3=FE(37.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCCTGATGGATTTGGTGGA
R:
TGCTGATTCATGAGCATCCGA
Band lengths:
246-937
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types