DreINT0111499 @ danRer10
Intron Retention
Gene
ENSDARG00000011886 | pdca
Description
phosducin a [Source:ZFIN;Acc:ZDB-GENE-031023-1]
Coordinates
chr2:21229233-21229670:-
Coord C1 exon
chr2:21229605-21229670
Coord A exon
chr2:21229379-21229604
Coord C2 exon
chr2:21229233-21229378
Length
226 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
GTGGCAAAACCTCTTTGTAGGGC
3' ss Score
3.53
Exon sequences
Seq C1 exon
GTCTTCATAGAAGATTCATCATGTCAGAGTCACCTGAGATTGAGGAACTACCAGCAACCCAGACAG
Seq A exon
GTAAAAAAAAAAGCCCTTAGAGTTTCACAGCAATTTCAGAACTCGTCTTACAAACATCAGTATTTACTGTAATCATGAGGTAATAGTGGAGATTTCCCACATGTTGTGATATGGCCAAGATTACTTTAATTGAAGGTTATGGTCAGTATCTTGTAAACAGTTTATTATTATTATTATTATTATTTAATTAACCCATTGATTGCAATGTGGCAAAACCTCTTTGTAG
Seq C2 exon
GGCCAAAAGGTGTCATCCATGATTGGAGGAAGTTTAAACTTGAGAGTGAAGACCATGAAAGTATCCCTTCCAACAAGAGAGAGCTCCTCAGACAGATGTCCAACCCTAAATCCAGTGATGACCCACGGGAAAAAGTGAACCGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011886:ENSDART00000149989:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.796
Domain overlap (PFAM):
C1:
PF0211411=Phosducin=PU(6.0=87.5),PF057696=DUF837=PU(6.4=37.5)
A:
NA
C2:
PF0211411=Phosducin=FE(20.6=100),PF057696=DUF837=FE(51.1=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:
AGAAGATTCATCATGTCAGAGTCACC
R:
CTTGCGGTTCACTTTTTCCCG
Band lengths:
204-430
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]