BtaINT0109217 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012945 | PDE6A
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:HGNC Symbol;Acc:HGNC:8785]
Coordinates
chr7:63254447-63255222:-
Coord C1 exon
chr7:63255133-63255222
Coord A exon
chr7:63254588-63255132
Coord C2 exon
chr7:63254447-63254587
Length
545 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
GTGTTTTTGTATTTCTTCAGATA
3' ss Score
10.68
Exon sequences
Seq C1 exon
ATTCTTCTCAAGTACCTCAATTTTGCAAATCTAATCATGAAGGTGTTCCACCTGAGTTACCTGCACAACTGTGAGACTCGGCGTGGCCAG
Seq A exon
GTAAAGGGCTTGACTTGAGGGAATGGACTGGACTGAAGGTGTCCTCTTCCTGAAGCACTGATGTGCTCAGCTAGAAGGCAGTAGTGACAGGAGTGCCTGGGAAGTATCGTGCAGTCTCTCCCAGCATCCCTGGGGTGCATGAGTCATGATGTCTGTAAAGCTGTAACCCAGAGTGACTGCACGTATAAGCTTTCATGTCAGCCAGCTTGTACTTGAATCCTTGCTAAGCCATTTACCAGTTCTAAGACCTTGAGCAAACCATTTAACCTCTCCAAGCTTCAGCCTCCTCTTTTGAAAAATGGGGATAATTACGGGATAAAGTATGTAGGATACTTGGGCTCTGTCAATGTTTGTTATCATCGTTGTTATTAACAACCTAGGAAATAAAAGAATTGGAAAGAGTTGGATCCAATAGCAGCTGCCCCGTTATTCACCACTCTGAAGCTCAGTTTCTCCATCTACAAAACAGGGACAGCTATTCTTGGTTATTATGAGCTGCTGTTGAGTGCCTCAGGAACACTAACTGTGTTTTTGTATTTCTTCAG
Seq C2 exon
ATACTGTTGTGGTCTGGGAGCAAAGTCTTTGAAGAGCTTACAGACATTGAGAGGCAGTTCCACAAAGCCCTGTACACAGTCCGCGCCTTCCTCAACTGTGACAGATACTCTGTGGGGCTCTTAGACATGACCAAACAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012945:ENSBTAT00000036662:3
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=PD(8.0=40.0)
A:
NA
C2:
PF0159021=GAF=PU(18.0=68.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTCTTCTCAAGTACCTCAATTTTGC
R:
TTCTGTTTGGTCATGTCTAAGAGCC
Band lengths:
230-775
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]