RnoINT0109243 @ rn6
Intron Retention
Gene
ENSRNOG00000009565 | Pdk4
Description
pyruvate dehydrogenase kinase 4 [Source:RGD Symbol;Acc:69061]
Coordinates
chr4:30554124-30555623:-
Coord C1 exon
chr4:30555482-30555623
Coord A exon
chr4:30554196-30555481
Coord C2 exon
chr4:30554124-30554195
Length
1286 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGG
5' ss Score
9.68
3' ss Seq
CAAAACTTCTCCCTTTCCAGGTA
3' ss Score
10.26
Exon sequences
Seq C1 exon
GTTCAGAAAATGCCTGTGAGAGAACTTCTTTTTCTTTTCTTCGGCAAGAATTGCCCGTCAGACTTGCCAACATCCTGAAGGAGATTGACATCCTCCCTGAACGCTTAGTGAACACCCCTTCCGTCCAGCTGGTGAAGAGCTG
Seq A exon
GTAAGGCTCGCTGCTCTGAAGTCTCTGGCTGAGTACTGCTTCTTATACATATTAACCTCATACCTGGATAACAGGCGGTCTTGACAGAAAAAAGTTTTGAATGTTGTACATAGGTTTGTATTAACTTAGGGCAAGTTATCATTAGGATTGTTATAAATCTGCAAATAGATGTCTATTGATATCCTAAAAAAAAATTCCTCTTCACCTTGGGGAGGATGTGTTTCTAGTTTTGCTTTTCTTTCCTTTTCCTCTTTTCCTTGCTGTTATTTGTCTCCCAAGACCAGGTCTGTGAGTCACAGGCTTCCTGAGATTTCTTATATAGTTAGGATGACCTTGAACTCCCTTCTACTTATCTTTACCTCCTAGCTGCTGCGATTATAAACATGGTCTACCATACCCAACTTCACTACAACATAATTTGGACACATGGGATAGTTTTGAAGAATAACCAACATATGGATTTTTTTTAACTTCGTGCTTTACATAACAAAAAAATGGAATCTGGAATTGTATAAACAATCCCCTGCCTAGAAATAGATGGAGATGTCTGCTGTTTAGAGAGGGTCTATGTTTTGTTCCTTATCAACAACTAGCAAAGTGAGCCTCGGGTTCAAATTGTGCCTTTGCATTTCCCTTAGTGTCTTAGCAATTGCGTTAAACCCTTGCTGCCTCAACAGCCCCACCTATTATTACAAGAGATGCTGCATATAATTAAAGGGAGTGATTTATTTCTTATCCAAACAAAGCAAGCACACGACCAGCATGGAGTCTCAGTTACTTTGATTTCGTCTTTGAGCTTCAAGTACTGAGCCTAGCAAGCAGCTGTTTGTAAGGTAGATTCATGCCATAGACTGTGGGAGATGAAGAGCCCTAGCCTAGTCCACTGACTGCACAGCATATCATCCAGTGAGTGAAGAAATATGGGGCACCAATGGGAAGATTCTGATCTCAAATGTTCTGTGTAGTAGCTCTGTGTAGTCTGCTACTGTCAAGACTTCAACCCTCCCACAGAGGCATACAGTCGGAAAAATAAATCAGAAAGGATTTCTTAAAGGTTGATTCAGAGTGTTTTTAGTAAAAGAAATGAAAACATCTGCCAATCGAAGTGGCTGGGAAAATAGACGATGGAAAAACGGCAGCTTTAAGACTATCTTAACCTACTATTCTCCAAGCATTTGGAAGGAAAGTTTCCATTTGAAACATAGTGGATCCCTTTCTCTTTCTAGTCATTTCTAAAGCTATTTTCATTGCATCTGACACTAGTTTCAAAACTTCTCCCTTTCCAG
Seq C2 exon
GTACATCCAGAGCCTGATGGATTTAGTGGAGTTCCACGAAAAGAGCCCAGAAGACCAGAAAGCTCTATCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009565:ENSRNOT00000012760:2
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(28.7=100),PF0160215=Adaptin_N=PU(29.7=56.2)
A:
NA
C2:
PF104364=BCDHK_Adom3=FE(14.6=100),PF0160215=Adaptin_N=FE(26.4=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:
GTTCAGAAAATGCCTGTGAGAGA
R:
GAGCTTTCTGGTCTTCTGGGC
Band lengths:
207-1493
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]