DreINT0111809 @ danRer10
Intron Retention
Gene
ENSDARG00000000380 | pde6a
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:ZFIN;Acc:ZDB-GENE-030616-42]
Coordinates
chr14:24711030-24712591:-
Coord C1 exon
chr14:24712508-24712591
Coord A exon
chr14:24711196-24712507
Coord C2 exon
chr14:24711030-24711195
Length
1312 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
ACTGCTCATCCCTCTTGCAGGAG
3' ss Score
11.6
Exon sequences
Seq C1 exon
CCCATGATGGACCGGAACAAGGCGGAGGAACTTCCCAAACTGCAGTGTGGTTTTATTGATTTCGTCTGTTCTTTCGTTTACAAG
Seq A exon
GTGAGGTCCTCCATTTCGATTAGCAAACAAAACGACATATGAGGCTTCATTGATCTACCCTTCTAAATGTTCACAGGATCCAGACGAGAGTCCATCAGGAAGCAGATACATAATCATGAGCAGAAAAAAAACAGTGCTGGTCTTGATCAGTTGTCGGTGTACTTGAATTTTATTGACTGAGAATGTCAGAATGCGTCAGATGAGTAGGGATGGATTAGGGAAATTTTTTCAAGCATAAAAAAACAACTATTATTTTATTTGAAATATTTACATACCATTCAAAGCATTCACAAATTTGAGTTTTTCAATATTAGCCTATAATATAATGATAGGATGTGCAAGGGATGTGCAAACATCTATGCTAACAGATAAATCATTCCTAGAATTTCCTAGATTTTTTGATCGAATATGGATCTGGACATTCTACAACTTTCTTGCAGCTGTAGATTAATATTTGAAGGTTAATTTTATTATAAAGTCATATTTCTTTTTTTATTATTATTTTTTTATTTTATTTGTAAAATATGAATCTCACAGTGTTTTTCATGCAATTGTTCTATCAGTGTAAATACATTCATGTCACCTCTAAGCTGCATTAAAAGTTCTAGATCCAGAAAGTATTGTTATATTGTAACTATATTGAAATGTAAACCTAAGGATCAACTTGATTGATTTTCTCTCCTACTATACAGTATTGCTAAGTTTTGTTGTGGTTTGATAAATGTAATTAAAGGGTCAGTTCACCTTAAAATAAAAATTGTCATAATTTTCCCTCATGTTATTCCGAGCTTTAATAATTTCTTTCATATTTGTGACAGAATCTTTTTTTATATAAGATCTGGAATATACACATATGTTTTTTTTTACTAAATGTCATTTTGAAAGTCATTAAGTAGGTTCATTTTGACTTTATTTACGTATAAACATTGAACTTCAAACTCAAACAAAAGCTTAACATTGGTTCTTGTAGAAATCCTTCAAAAACATTTTGAAGTGTCAAAGTTTTGGGTGAGTAGACTTTCAAATGTGCACCATAAATCCCTCTGATTGATGAAAAAAATCTACATTTGTAGTTTGAAGATACATTTCATTTAGATTTTAAATGTAATGGTAAATAAAAAGTAACAGAATTTTCATTTTGAGGTGAACTAGCCCTTTAAATGAGTTGTTTACATTAAAATTGATCTTATGACCACTAAAAATGCTTAGACTAGCCTTTAAAATGTAATAACATCTAGTATGTCTGAAATTCCTCAACGTTTGAACCCACCAACATGACTCCCTCTTGACTGACTGCTCATCCCTCTTGCAG
Seq C2 exon
GAGTTTTCTCGCTTCCATGTGGAGATCACACCAATGCTGGAGCGTCTGCTGAACAACAGAAAAGAATGGAACGCACTGAAGGAAATACATGAGGCCAAAGTAGCCAAGCTGGATGAGGCCAAAAAGGCTAAAGAAGAAGCACATGCTAACTCAGATCATAAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000380:ENSDART00000000392:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.304
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(10.8=100)
A:
NA
C2:
PF0023314=PDEase_I=PD(7.6=33.9)
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:
CCATGATGGACCGGAACAAGG
R:
TGTTTATGATCTGAGTTAGCATGTGC
Band lengths:
247-1559
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]