DreINT0112057 @ danRer10
Intron Retention
Gene
ENSDARG00000054848 | pdk4
Description
pyruvate dehydrogenase kinase, isozyme 4 [Source:ZFIN;Acc:ZDB-GENE-060503-754]
Coordinates
chr19:41612517-41612824:-
Coord C1 exon
chr19:41612735-41612824
Coord A exon
chr19:41612595-41612734
Coord C2 exon
chr19:41612517-41612594
Length
140 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACA
5' ss Score
8.1
3' ss Seq
CTGCACTTTTCTCTCTCTAGATG
3' ss Score
11.02
Exon sequences
Seq C1 exon
CGTTAATCTTTGATGGCAGCACCAATCCAGCCCACCCCAAACACATTGGCAGTATCGACCCAAACTGTGACGTTGTAGAGGTCGTCAGAG
Seq A exon
GTAACAAACCCTGTTTCTTTTCTGGGTAATACTGTTCATTCTTTGAAAGAAAGCTAATAAAGTTATTTTATGAACACTTGAAATAGCCTGTATATTGTTTGACTTGTAAGCTTAGTTTTGCTGCACTTTTCTCTCTCTAG
Seq C2 exon
ATGCCTATGAAAGCTCCAAGATGCTGTGTGATCAGTACTACTTGACCTCTCCTGAAGTGGAAATCAAACAAGTGAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000054848:ENSDART00000145135:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.098 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF104364=BCDHK_Adom3=PD(12.4=64.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTTAATCTTTGATGGCAGCACC
R:
CACTTGTTTGATTTCCACTTCAGGA
Band lengths:
164-304
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]