DreINT0111801 @ danRer10
Intron Retention
Gene
ENSDARG00000000380 | pde6a
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:ZFIN;Acc:ZDB-GENE-030616-42]
Coordinates
chr14:24721816-24722611:-
Coord C1 exon
chr14:24722504-24722611
Coord A exon
chr14:24721926-24722503
Coord C2 exon
chr14:24721816-24721925
Length
578 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGA
5' ss Score
6.66
3' ss Seq
CAGTTGTAATGTTATTTCAGACA
3' ss Score
2.93
Exon sequences
Seq C1 exon
ACTCTGGTGCGTTTTGTGTATTCTGTCAGCAAAGGCTACAGGAAGATTACCTACCACAACTGGAGGCATGGCTTCAACGTTGGCCAGACCATGTTTACACTGCTTATG
Seq A exon
GTAGGAGAAAACCCTTACACAATGACATTACAAACGTTTCCATTCTAGACTCTATTAAGGCAGCTCTCAAAAAAACTCCTCATCTCAGCTATGAGGCTTCATCTTGCTCATCATTGACTAGTCAGACCTTGCCATTTACACTAACAAACATGAAAAATGTTTGAACAAGCTTGTTAGCCTTGTAACTGGGCATTTGATAAATTTACCCTAATGGTTGGTTGTGTGCTGGATTCATGGATCTTTATAAGAAAACTTGTTTAATGATACAGCCCACCTCTAGCACATATTCTCTGAAATGGCAGACGGCCCCTTCAAATTAATCAGTGAAGTGTAAACCTGCTCCTGGTTAAGTCATGTGTAATCACAGTGATCTGGCCGTTCGTCAGGAAGGAAGGAGTGTTGGAAGGCCGCAAGAAACGCAAGCCAGGCTGCTAATGAGCCTTTCTCAGCACTACTCCCATGCTTCACAGAGTCTAATGAGCCCTCACTAGTCAGCATTAAGCTCTACAAGAGCAGGGTGTGTGTGTTGAGGATGCTCCAACTTGAAGCCTATTAAACCAGTTGTAATGTTATTTCAG
Seq C2 exon
ACAGGTGACCTGAAGCGTTACTATACGGACCTGGAGGCGATGGCGATGGTGACCGCTGGACTCTGTCATGATATTGACCACCGTGGCACTAACAACCTCTACCAGATGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000380:ENSDART00000000392:13
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:
PF0023314=PDEase_I=PU(7.2=50.0),PF0771711=OB_NTP_bind=PU(6.4=19.4)
A:
NA
C2:
PF0023314=PDEase_I=FE(14.5=100),PF0771711=OB_NTP_bind=FE(32.7=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:
ACTCTGGTGCGTTTTGTGTAT
R:
TCTGGTAGAGGTTGTTAGTGCCA
Band lengths:
214-792
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]