BtaINT0109528 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008744 | PDK2
Description
Bos taurus pyruvate dehydrogenase kinase, isozyme 2 (PDK2), transcript variant 1, mRNA. [Source:RefSeq mRNA;Acc:NM_001159481]
Coordinates
chr19:37183008-37183377:-
Coord C1 exon
chr19:37183288-37183377
Coord A exon
chr19:37183086-37183287
Coord C2 exon
chr19:37183008-37183085
Length
202 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
ATGACCTCTGCTTCTCTCAGATG
3' ss Score
8.58
Exon sequences
Seq C1 exon
CCCTGCTCTTTGACGGCAGAACCAACCCTGCCCACCCCAAACACATCGGCAGCATCGACCCCAACTGCAATGTCTCTGAGGTGGTGAAGG
Seq A exon
GTGAGTCGTCCTCACTGTGCCTGGCCCACAGAGGAGCCCCAGTGAACCCCCAAGTTTACCTGGCCAGAGGGTGACCCATTCCCCAGTGGGTGGGGGCCACATCCCCATGGGTTTAATGTTGGTGGCACCCACTGTTGATACCAAGAGAATTGCCTGCTGTGGGGAGGCCACCCCATTCTCTGATGACCTCTGCTTCTCTCAG
Seq C2 exon
ATGCCTACGACATGGCCAAGCTCCTGTGTGACAAGTATTACATGGCCTCTCCTGACCTGGAGATCCAGGAGATCAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008744:ENSBTAT00000034924:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.161 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF104364=BCDHK_Adom3=PD(12.1=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:
CCTGCTCTTTGACGGCAGAAC
R:
CAGGTCAGGAGAGGCCATGTA
Band lengths:
148-350
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development