RnoINT0109244 @ rn6
Intron Retention
Gene
ENSRNOG00000009565 | Pdk4
Description
pyruvate dehydrogenase kinase 4 [Source:RGD Symbol;Acc:69061]
Coordinates
chr4:30553221-30554195:-
Coord C1 exon
chr4:30554124-30554195
Coord A exon
chr4:30553406-30554123
Coord C2 exon
chr4:30553221-30553405
Length
718 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGA
5' ss Score
5.73
3' ss Seq
CTATAAATGTTCCGGCTTAGCTT
3' ss Score
4.22
Exon sequences
Seq C1 exon
GTACATCCAGAGCCTGATGGATTTAGTGGAGTTCCACGAAAAGAGCCCAGAAGACCAGAAAGCTCTATCAGA
Seq A exon
GTAAGATTTCTTCTTGAAAACACTTCCTTAGAAATCTGGATCTTTCAGGATGCATCTCACAGACTGTTTTAAGCTTAAAGAGCCCCAGCCTTTCACAATAAGTTGCTACCCCTTACAAATGTTGGCTTGCTTGTGGTTTTAGAAGTGGAGAAGTGTAGGGCTGAAATTAATGCTAGGTGGGAACCACTGAAAAGGACTTGGAGCTTTTGATCTTCAAAGGGTGCCATGCTTACTTTAAATTTAGGCCAAAGATGATATTTGCAAGAGAGTTTGCCGTAACACAACATTAATGGACTTCTGGGTCGTTAGTGACTACATATTTTCTTTTCGTGTGACAATTTCTATCTAGCTAAATAGCAATCTTTTTTAAAAATCTCTGGTTTTATTTTTCCACAATGGCATGCCAGAATCCTCTTTGATTTTTCACAATAGTCTCTAACAAGTAGACTTAATGAACATTTTAGTGAAGACAGTAGTCACACAGTGAGTAGTTTGATATGGGATTTGGAAATACAAACCCTTCATGAAGCTGCCTCTTCTGCTACTGTAGAAGAATGTATAGTGAGAGTCCAAAAGGAATTTCCCCCAGAATTTTATAATTGGCTGTGCCATTAAGTTGGTCTTGCAAAAAGAGCTTTAGTTTTCTCTGAAGTAACTCAAGGAAGAGATGTGAGGCGAACTTCTTTAATATCCACTAACTATAAATGTTCCGGCTTAG
Seq C2 exon
CTTTGTAGACACGCTGGTCAAAGTTCGAAACAGACATCATAATGTGGTCCCTACGATGGCACAAGGGATCCTGGAGTACAAAGACAACTGCACCGTTGACCCCGTTACCAATCAAAATCTTCAGTATTTTTTGGACCGGTTTTATATGAACCGCATTTCTACTCGGATGCTCATGAACCAGCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009565:ENSRNOT00000012760:3
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(14.6=100),PF0160215=Adaptin_N=FE(26.4=100)
A:
NA
C2:
PF104364=BCDHK_Adom3=FE(37.8=100),PF0160215=Adaptin_N=PD(42.9=61.9)
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:
GTACATCCAGAGCCTGATGG
R:
TGTGCTGGTTCATGAGCATCC
Band lengths:
257-975
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]