GgaINT0041686 @ galGal3
Intron Retention
Gene
ENSGALG00000006626 | PDE6C
Description
NA
Coordinates
chr6:21457273-21458595:-
Coord C1 exon
chr6:21458512-21458595
Coord A exon
chr6:21457427-21458511
Coord C2 exon
chr6:21457273-21457426
Length
1085 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
AAATTCAATTGCTTGCATAGGAA
3' ss Score
4.79
Exon sequences
Seq C1 exon
CCCATGATGGACAGAAACAAAGGTGATGAACTACCTAAGCTCCAAGTTGGTTTCATAGATTTTGTGTGCACATTTGTGTACAAG
Seq A exon
GTAAGAACATTTTTTTGTTTGTTTATTTTCCCACTGAAGTAGTTCTGGAACAACTAATGACCAACAGTTGCACTAAAAAATTTTTAGACAGTTGAAGGATTCTTATTTATTGGGTAAACTGCTATTACTACCACCACATTTTTTTCAGTCTTTTAGATTTAGAAGAAATTGCTCTTACAAAGCAAATTCAAGACATGGTTACCAAGAGAAGATCTCAGTGTAACTTGAGGGCTCTAAGTTATTGTTACTACCTTCCTTGAAAGACTGAATTAGAAAGCCCTGGTTCTTTAAAGTCCCATTTAATATAAATATGTGACATGTAGATGGTTACAGAAATCAGTTATTGGCACACATAAAGGAACAGAAAATTTACAACGTTCTATAAGCATAGCCATTGTATATTTTCGGGAAAGCACTTTAATGTCAACTTTCTTAATCTTCATTTAGCATTTAACATTATCTCAAAATGTTACACAGAAAAGAGTCATGCAATATTTCAGCATCTTTAGGTACATCCTAATCTGCCCGGAATATACTACAAAATACTAGACTTTCTCTATATCCTGATATTGATAAACATATCAGGAAATATCAGGTATCAAAGTTATAATTTTATTATATGAACCAGAATTTCAAATGTGAAATTAGGGAAGATACTAAAATGTGCAGCATATAATTCAGATCTATTCCAACACTATGTGTACAAAATGGCATTACTATCCCAGCACAATCTTTTCAATAATATACCACCACTGCTTGGCCAAAGACACGCTTGCAAACATGCACTGGCAGACAGTGGCATTATTTTAAAACTTCTTTTCAATTCTATAGAAAACCAGCTAACAGAAATGGAACAAGTAGTTGCAAAACAAACAAACAAACAAACAAGTCAAAACCACAAACTATCAATTAAAATTAATTCATCCAGCACACAAACAGAAATAATAGAATTTTTAATAGAACTTTTAATAGAAAAATTAAAGCAAATGCTTTCTCCGCAAAGCAGCATTTCCAGAAATCCATACTTTACAAAGTATGGTAAAGTTGTCATATTTCTAATTCATTAAATTCAATTGCTTGCATAG
Seq C2 exon
GAATTCTCAAGATTTCACAAGGAAATTACACCCATGTTCGATGGTCTTCAAAACAACAGGGTTGAATGGAAAACAAGAGCTGATGAATACGAAGAGAAGATGAAAGTTATTGAGGAACAAAAGAAAAAGGAAGAAGAAGCAGCTGCCAAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006626:ENSGALT00000010702:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.214 A=NA C2=0.346
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(10.8=100)
A:
NA
C2:
PF0023314=PDEase_I=PD(7.6=36.5),PF141951=DUF4316=PU(87.5=80.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCATGATGGACAGAAACAAAGG
R:
GGCAGCTGCTTCTTCTTCCTT
Band lengths:
231-1316
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]