BtaINT0112612 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010195 | PKN3
Description
Bos taurus protein kinase N3 (PKN3), mRNA. [Source:RefSeq mRNA;Acc:NM_001205566]
Coordinates
chr11:99234451-99235042:+
Coord C1 exon
chr11:99234451-99234691
Coord A exon
chr11:99234692-99234896
Coord C2 exon
chr11:99234897-99235042
Length
205 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
GCCCCACACTCTGCACACAGAGC
3' ss Score
7.03
Exon sequences
Seq C1 exon
CCTGGGGCAGGCCATCAGCCCCTGGAGGATGAGAAAGAGGTGATCCGCCGGGCCATCCAGAAGGAGCTGAAGATCAAGGAGGGTGTGGAAAACCTGCGGCGGGTGGCCACAGACCGCCGCCACCTGGGCCACGTGCAGCAGCTGCTGCGGTCGTCCAACCGCCGCCTGGAGCAGCTGCATGGGGAGCTGCGGGAGCTTCACGCCCGTATCCTGCTGCCCGGGCCTGGGCTGGGCCCGGCTG
Seq A exon
GTGAGTGAGGAGCACGAGGAGGCCCCTCGGGACGGGAAGTGCCAAGTTGACCCAGCTCCTTGATCTTGGCTCTGATCTACTCTCAGAGCTTCTCTTGAGAGAGCCCTGCCCAAGAGAGTTGGAGAGGAGCAAGCGAGGCATTGGGGGGTGGGGAGGGCTCTCGGCTCTGGGGCAGGCATTCATGTGCCCCACACTCTGCACACAG
Seq C2 exon
AGCCCGCGGCCTCAGGACCTCGGCCGCTGGCCGAGCAGGCAAGGGCTCGGCACCTGGAAGCTCTACAGAGGCAGCTGCAGGTGGAGCTGAAGGTCAAGCAGGGGGCTGAGAACATGACCCACACCTACGCCAGCGGCACTCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010195:ENSBTAT00000013461:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.704 A=NA C2=0.755
Domain overlap (PFAM):
C1:
PF0218511=HR1=WD(100=82.7)
A:
NA
C2:
PF0218511=HR1=PU(43.8=65.3)
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:
GCCCCTGGAGGATGAGAAAGA
R:
TGCCTCTGTAGAGCTTCCAGG
Band lengths:
297-502
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development