DreINT0111812 @ danRer10
Intron Retention
Gene
ENSDARG00000000380 | pde6a
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:ZFIN;Acc:ZDB-GENE-030616-42]
Coordinates
chr14:24731370-24732008:-
Coord C1 exon
chr14:24731868-24732008
Coord A exon
chr14:24731445-24731867
Coord C2 exon
chr14:24731370-24731444
Length
423 bp
Sequences
Splice sites
5' ss Seq
AAAGTGACT
5' ss Score
1.17
3' ss Seq
TTGTTTTTGTGTATTTGTAGGAG
3' ss Score
8.99
Exon sequences
Seq C1 exon
GTATTGCTCTGGTCTGCCAGCAAAGTGTTTGAAGAGCTGACTGACATTGAGAGACAGTTCCACAAGGCTCTTTATACAGTCCGAGCTTTTCTCAACTGTGACCGCTACTCTGTTGGCCTTCTCGACATGACCAAAACTAAA
Seq A exon
GTGACTATCTTTCTATCTTTTTATCTGTCTAGCACTAGCACAACAACTAGCCAAGCTATACTAACAAGATGTTAAATGCTAGCAACATGATAAAATGCTAGCTACATGCTAAAAGTAGGCTAGCAATGTACTAAACATGTTAATGTGAATTTGTGCTAACATAATTAGAATATGTCTGTGTCTGGCTGTCTGTCTGTTTGTCTGTCACTAGCAATATGTTTAAATAAACCTCTTTCTAACAAAAAAAATTTTTAAATAAACATCTTATAAGCTTGTTTACTGCTGTTACACTTGCAAAATTTAGTACTTTGATATGTCATTTGAACCATATTTGAATCAGTTGAATTTATAATGAATATATGGCACTTGTGCCTATTTAAACATATGTTTGCCTTAAAATATTTTGTTTTTGTGTATTTGTAG
Seq C2 exon
GAGTTCTTTGACCTTTGGCCCGTACTGATGGGAGAAGTACCTCCATATAGCGGACCAAAGACCCCTGATGGCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000380:ENSDART00000000392:4
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(18.0=68.1)
A:
NA
C2:
PF0159021=GAF=FE(13.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTATTGCTCTGGTCTGCCA
R:
TCTGCCATCAGGGGTCTTTGG
Band lengths:
216-639
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]