DreINT0111817 @ danRer10
Intron Retention
Gene
ENSDARG00000000380 | pde6a
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:ZFIN;Acc:ZDB-GENE-030616-42]
Coordinates
chr14:24727273-24729533:-
Coord C1 exon
chr14:24729384-24729533
Coord A exon
chr14:24727417-24729383
Coord C2 exon
chr14:24727273-24727416
Length
1967 bp
Sequences
Splice sites
5' ss Seq
GAGGTATTT
5' ss Score
7.63
3' ss Seq
CGAATCCTTATTTATTTCAGTCT
3' ss Score
5.07
Exon sequences
Seq C1 exon
AAAGAACCTCTGGATGAATCTGGATGGATGATAAAGAATGTGCTCTCCTTGCCTATCGTGAACAAGAAAGAGGAAATCGTTGGCGTGGCCACGTTCTATAACAGGAAAGATGGAAAGCCTTTCGATGAAATGGACGAAACGCTAATGGAG
Seq A exon
GTATTTGAGGCCACAGTATAGACCAGTAGTGTGTCATGGCTAAATTTACAGTAATGGATGGATCGGCAGACACTGCATTATTCATTCACGGTGTGTTTGCCCCTTGAAAGTTTGCAATGTTCTTAGTCTATTATGCTTAGCTTGGTAGGATTGAATTAAATCACTAAACCAAAGTTTTAAAACTCAAAAAAGTGCCCAGTTTTTCTGAGGGCGTTTGAGTTGGAAAAAAACATTTGGACGTGTGTAATTTTATCTCAGTGTCAATTGGAACAGTTTGAAAATACATCTTATATTTAATTGAAATGAATCAGAACCTGAATCAACTTTTTTCTGAATCTAAATCCATAAACCTCAACCAGAAAATAAACATTAATATATGTATGATTCTAAAATGGGAACGAAATTTAGATCTAAACCTGCATGTCTAGTAAATGTGAACCTGAATTCATCCTAAATGTGAACCTAAGCGTAAATATGAAACTTAATACGTATTTGAACCTGAATCTTAATCTACAGTTTATTTGAACCTGAATGCAAATCTTAATCTAAACATAAGTTTAAATGTTTGAGTTTGAATCTCAATCTTAAAGTGAGATGTAATCTGAAATTCAATCTGAAATTTAATCTGATTAATTTAATCTGAATTTTAAACTGAATTTAAAACTAAACCTGAATATCGATTTTATTATCAGCCTGAACTCTATTTTGAATGGCATCTAAATCTAACTCTAAATCTCAACCAAAGAATAAATATGAATTCTAAACCTGCATCTGAATTAACATCTGGACCTGTGGCCAATTGCACCAGCAGTGCGTGAGTTAAAACGTAGCCTAGTTGTGACTTAAAGGGACGCTAAGTTATAACTTACATACACCTAAATATTTTTGTGGCACTACTGAACTTAGTTTAAACGTAACGCTACGTTCCAACTAAATATTTAGCAGCCTCCCCCATGTATAATGGTGGAAAAGAGACGACAGCCAGATTAGTTTACTTTGAGGAGCTTGCGATATGATAATGAAGAATGATCTCCTTCTACTCAAAACTTTAATTTCCTCCTAAATCTTGCATTGTTTTAGTTTGTGAAAGAAGAGTTTAATTTTCTTTCAAGGAGTGTTTTCTGTTAATTGTATCCATCAATTAAAACAAGAATTTTTTTTATGACTGAGTTCTTCTCCCTGCTCTTTTCTCTTTCATGATATATAAATAAAATCTAGTTTAAAGTTTTCATAACTTCATGTGTATTTTGCGTGCATTCGTGGCTCACAATGCTGGTATGTGCGTCATCTGCTAAAGTGACAGACTATAATGTAATCATGTTCTATAAAAATGTAATTTGTCATTTCCTTTTTTTTTAAAGGAAAATTATGTATAGACACATTAGTTACAGAATATTAAAGCAGTTTAATGATTTAAATGCTTCTTATTGGATATTACGTCATTCAATGTGACTACACATGACTTTACAGAGAGCTTACGGCCCACTAACTACAGTTTGCCCTAAGAATATGTGGTGCATCCAAAGTAAAAACTAATTTAGTTACAAACTAGCTAATAGTTAACTTTACATGGACTTTATGTGGACTTTATGCCGTAACCTCAATCTCAATTTAAATGTAAACCTGAGTGTAAATATGAATCTGAACTTAAGATGTTTGTTTAAATGTGAATTTTAAATCCTGATATGAATCTTAACCTAATTGTAAACATTATTTTTAACATTTTGTAAATCTAAATTGAATCTAAATAAGATTCTCAGTCTACAGTAAATGTGAATCTGAAACTCATCTTAAATTTGAACGTGAATATAAATGTGAAGTCAAACCTGAATTTGAATGTGAATTTAAACCAGAATCTTAACCTAAATGAGAACATAAATGTAAAGAAAATTGTTTTATCAAATTTGAATCTGAAATTAAATCTCAACTTAAAGGTGAATCTAAACCCGAATCCTTATTTATTTCAG
Seq C2 exon
TCTCTCACTCAGTTCCTGGGATGGTCAGTGCTGAATACAGACACATACGATAAGATGAACAAGCTAGAAAATCGTAAGGACATCTTTCAGGACATGGTCATGTACCACGTCAAATGCAGGAAGGATGAGATTCAGAATATCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000380:ENSDART00000000392:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(27.5=100)
A:
NA
C2:
PF0159021=GAF=PD(5.1=18.8)
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:
AAAGAACCTCTGGATGAATCTGGA
R:
CAAGATATTCTGAATCTCATCCTTCC
Band lengths:
294-2261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]