BtaINT0112617 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010195 | PKN3
Description
Bos taurus protein kinase N3 (PKN3), mRNA. [Source:RefSeq mRNA;Acc:NM_001205566]
Coordinates
chr11:99236372-99237703:+
Coord C1 exon
chr11:99236372-99236499
Coord A exon
chr11:99236500-99237519
Coord C2 exon
chr11:99237520-99237703
Length
1020 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGA
5' ss Score
5.24
3' ss Seq
TGCCCGTATGCCTCCTGCAGGCT
3' ss Score
8.54
Exon sequences
Seq C1 exon
GTCCTGAGCTGATGGTAGAGGAGCTACGGCACCGTCTACGCATCGAGGCTGCTGTGGCCGAGGGTGCCAAGAACGTGGTGAAGCTGCTCGGTAGCCGGCGAACGCAGGACCGCAAGGTGCTGGCCGAG
Seq A exon
GTCAGACCGTGCTTCCTGTCTGACTGGTACCACCCTTTGTAGTGGCCATGATACCGCTCGACGGGTATCATGGACCACATGAGCAATGGCCATGAGGAAACAGGAGGCACATTCTTTTTATATATATAATTTTCTTTCTTTCTTTCTTTTTGGCTCTGCTGAGTCTTTGTTGCTGCTTGGGCTTTTCTGGAGTGGTGAGCGGGGGCTACTCTCTAGTTGCGGTTCGTAGGCTTCTCACTGTGGTGGCTTCTCTTGTTGCAGAGCACAGGCTGCAGGGCACAGGGATTCAGGGCTCAGTAGTTGTGGCTCTCAGGCTCTAGAGCACAGGCTCTATAACTGTGGTGCGTGGCTTAGTTGCCCCAAGGCATGTGGAATCTTCCCAGACCAGGGATCGAACCCATGTCTCCTGCACTGGCAGGCAAATTCTTTACCACTCAGCCACCAGGGAAGCCCAGAAGACACATTCTTGTCTAGATCAGGGGTCTCCAACTTCCAGGCCGCGGACCGGTACCTCCTGTCAGATCAGCGGCAGCATTAGATTAGAAGTAAAGTGCACAAAAATGTTGTTTAGCCGCTCAGTCGTGTCTGACTCTGCGACCACATGGACTGCAGCACGTCAGGCCTCCCTGTCCTTCACCATCTCTTGGAGCTTGCTCAAACTCATGTCCATCTAGTCACAGATGCCATCCAACCATCTCGTCCTCTGTTGTCCTCTTCTCCTCCTGCCCTCAATCTTTCCCAGCATCAGGGTCTTTTCTAATGATTCGGCTCTTCGCATCAGGTGGCCAAAGTATTGGAGCTTCAGCTTCACAAAAATGTAATGCGCTTGAATTGTCCTAAAACCATCCCTCCCGCCTCCAGTCCGTGGAAAAATTGTCTTCCACAAAACCAGTCCCAGCTATCAAAAAAAGTTGGGGACCACTAGTCTAGACCTCATCCAGAGTGCCTCTGGGTGGCCTGAACCACTGCCCCTGCCATTACCCCAGGGCCCTGTATCCCCTGCCCGTATGCCTCCTGCAG
Seq C2 exon
GCTCAGGCCCAGCTCCAGGAGTCCTGCCAGAAACTGGACCTCCTGCGGCTGGCCTTGGAGCAGCTGCTGGAGAGACTGCCTCCTGCCCACCCTCTGCGCGGCAGAGTGGCCCGGGAGCTGCGGACTGCTGCGTCTGGGAACCCACAGCCTTCAGGGACGCTCGTGAAGCCCACCGCCATGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010195:ENSBTAT00000013461:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.279 A=NA C2=0.435
Domain overlap (PFAM):
C1:
PF0218511=HR1=PD(2.7=4.7),PF0218511=HR1=PU(54.2=90.7)
A:
NA
C2:
PF0218511=HR1=PD(43.1=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCTGAGCTGATGGTAGAGGA
R:
GTCATGGCGGTGGGCTTC
Band lengths:
310-1330
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development