GgaINT0010613 @ galGal3
Intron Retention
Gene
ENSGALG00000004123 | PABPC1L
Description
NA
Coordinates
chr20:5198742-5199227:-
Coord C1 exon
chr20:5199137-5199227
Coord A exon
chr20:5198868-5199136
Coord C2 exon
chr20:5198742-5198867
Length
269 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
GTGCTCCATCTCTCCATCAGCGT
3' ss Score
6.75
Exon sequences
Seq C1 exon
CCGCAAACCAGAGCTGCTTTCTACAGCCCCAGCCCAGTTGTCCCTGTCCGTCCTGCCACTCGCTGGAGTGCGCAGCCCACCCGGCCTCCCC
Seq A exon
GTGAGTGCATCCATCTGTCCCTCGCTGTCAGCAGGGCTGGTTCAGGGACCAGGACACTCTCTTAAAGACACCACAAAGTGTGTGGCCGTGGGAAGCTGTCACCTGGGGAAGCATGCGGTGTCCTGATGTAGGGCTCACTGGTGGCAGGCACTGGGGCTCAGGCTAACCACAGAAACTTTCCCTGAGCGCAGCCACCTCCCAGCACATCTCCTCCAATGCTTTTTTTTTCTATCAGAAACTTCATTAATTGTGCTCCATCTCTCCATCAG
Seq C2 exon
CGTACCCTGCAGCCACACCCATCCTGAGGGCTGCTGTGCAGCCCCGGCGCCTGCTGTCCAACATCAGCACCATGAGACAGGCGTCCACCCAAGTGCCTCGTGTGCCCCCCCAGGCGCAGAGAGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004123:ENSGALT00000006565:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.677 A=NA C2=0.744
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CGCAAACCAGAGCTGCTTTCT
R:
CACTCTCTGCGCCTGGGG
Band lengths:
215-484
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]