BtaINT0109056 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008419 | PDE2A
Description
Bos taurus phosphodiesterase 2A, cGMP-stimulated (PDE2A), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_001256273]
Coordinates
chr15:52915729-52916191:-
Coord C1 exon
chr15:52916092-52916191
Coord A exon
chr15:52915842-52916091
Coord C2 exon
chr15:52915729-52915841
Length
250 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCT
5' ss Score
5.39
3' ss Seq
CCCTGTTCTCTCCCCGACAGTGG
3' ss Score
9.85
Exon sequences
Seq C1 exon
GATTATCAGCGCATGTTGGACCTGATGCGGGACATCATCTTGGCCACAGATCTGGCCCACCACCTCCGCATCTTCAAGGACCTCCAAAAGATGGCCGAAG
Seq A exon
GTGCCTGCCTCTAGCCTGGGTCTCTAGATCGGGGAAGGACCACCAAGAGGGGAACTCGCCTGGAGGGCACCCCCAGGGTTCAGACCCATCCCTTCCAACATCAGCCCACCAGGCAGACCCAGCTCTGCATCCCTGGCTCCCATCCAGGGTGCTGAATTCCCTGTGCCACTTTGGGATGGGCCCTGGGGCCTTGCTCTCAGGGACCCAGGATGCTGGGTTCCTCTCCTTGACCCTGTTCTCTCCCCGACAG
Seq C2 exon
TGGGCTATGATCGAACCAACAAGCAGCACCACAGCCTCCTTCTCTGCCTCCTTATGACCTCCTGTGACCTCTCTGACCAGACCAAGGGCTGGAAGACCACGAGGAAGATCGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008419:ENSBTAT00000011077:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(13.9=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(15.5=100)
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATTATCAGCGCATGTTGGACC
R:
GCGATCTTCCTCGTGGTCTTC
Band lengths:
212-462
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development