BtaINT0109066 @ 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
chr15:52928116-52928427:-
Coord C1 exon
chr15:52928375-52928427
Coord A exon
chr15:52928191-52928374
Coord C2 exon
chr15:52928116-52928190
Length
184 bp
Sequences
Splice sites
5' ss Seq
TATGTGAGT
5' ss Score
5.56
3' ss Seq
GCTGTGTCCCTCCCTCTCAGCTG
3' ss Score
8.9
Exon sequences
Seq C1 exon
GGGAGCTCTACGACCTGGATGCATCTTCCCTGCAGCTCAAAGTCCTCCAATAT
Seq A exon
GTGAGTCCCTGTGCCCCTACCACTGTGTTCCTCCCGGAACGGAAGTCCTCTTGAGCTTCCATCTCAGTACAGATTCAGATGTCCTCTCTTCTCCACTTACCTGCGAGCCTCAGAAAGGCAAAGGGTGGGGAGTGGGGATCTCCCAGATGCGAGGTCAGCCCCTCGCTGTGTCCCTCCCTCTCAG
Seq C2 exon
CTGCAACAGGAGACCCAGGCATCCCGCTGCTGCCTGCTGCTGGTATCCGAGGACAATCTTCAGCTCTCCTGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008419:ENSBTAT00000011077:9
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:
PF0159021=GAF=PU(8.3=61.1)
A:
NA
C2:
PF0159021=GAF=FE(18.2=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:
AGCTCTACGACCTGGATGCAT
R:
GCAGGAGAGCTGAAGATTGTCC
Band lengths:
122-306
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development