GgaINT0041671 @ galGal3
Intron Retention
Gene
ENSGALG00000006626 | PDE6C
Description
NA
Coordinates
chr6:21472557-21472782:-
Coord C1 exon
chr6:21472708-21472782
Coord A exon
chr6:21472622-21472707
Coord C2 exon
chr6:21472557-21472621
Length
86 bp
Sequences
Splice sites
5' ss Seq
CGAGTGAGG
5' ss Score
4.44
3' ss Seq
ATTTTTCTCTTTTTGTTTAGGAA
3' ss Score
10.37
Exon sequences
Seq C1 exon
GAGTTCTATGATGAATGGCCAATTCGGCTGGGAGAGGCAGAGCCTTACAAAGGTCCCAAGACACCTGATGGACGA
Seq A exon
GTGAGGATATTAATTTTTCTTTTAATGAATCTTAACTTTGACATTGAGTGTACAGGTAACTTAGATATTTTTCTCTTTTTGTTTAG
Seq C2 exon
GAAGTCAACTTTTATAAGATTATTGACTACATCTTGCATGGGAAAGAAGAAATCAAAGTCATTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006626:ENSGALT00000010702:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(13.5=100)
A:
NA
C2:
PF0159021=GAF=FE(11.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTCTATGATGAATGGCCAATTCG
R:
TGACTTTGATTTCTTCTTTCCCATGC
Band lengths:
135-221
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]