BtaINT0112603 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010195 | PKN3
Description
Bos taurus protein kinase N3 (PKN3), mRNA. [Source:RefSeq mRNA;Acc:NM_001205566]
Coordinates
chr11:99241344-99241811:+
Coord C1 exon
chr11:99241344-99241512
Coord A exon
chr11:99241513-99241708
Coord C2 exon
chr11:99241709-99241811
Length
196 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGTCTGCTTCTATCCCACAGTAA
3' ss Score
8.87
Exon sequences
Seq C1 exon
GTCAGGACTTCCTGAGGGCTTCCCAGATGAACCTCAGCATGGCAGCCTGGGGGCGCTTGGTCATGAGCCTGCTGCCGCCCTGCAGCTCCCCAAGCACCATCAGCCCCCCCAAAACGTGCTCCCAGACCCCAGCCACACCCCAGCGGGCCACCGACCCCGACTCGCCCAG
Seq A exon
GTGAGGAACCTCACTCACCCCAGGCTGCCTGCTTCTCTGCGGTGTCACCTCTCTCCAGACGCAGATGGAGCCTGCCCCGTGGCTCACCCTCTGACCTGTCTGTCTGTCTCGCGTGGCTGTGCGTCCACCCCCGCCCTCCCTGCCCGCCACTGTTCCAGCTGTCTGTGTCCAGTATATGTCTGCTTCTATCCCACAG
Seq C2 exon
TAACTTCCCACCCAAGAAGACCCCCTTGCGAGAAGAGATCCAACCCCCACCCAAGCCCCCTCGCCTCTACCTGGCCCAGGAGCCAACCCCCGAAGAGATGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010195:ENSBTAT00000013461:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.491 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTCCCAGATGAACCTCAGC
R:
ATCTCTTCGGGGGTTGGCTC
Band lengths:
251-447
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development