GgaINT0010616 @ galGal3
Intron Retention
Gene
ENSGALG00000004123 | PABPC1L
Description
NA
Coordinates
chr20:5197144-5197807:-
Coord C1 exon
chr20:5197714-5197807
Coord A exon
chr20:5197275-5197713
Coord C2 exon
chr20:5197144-5197274
Length
439 bp
Sequences
Splice sites
5' ss Seq
TAGGTGGGT
5' ss Score
5.56
3' ss Seq
TTCCCTGGTGCTTCGGGCAGGTG
3' ss Score
7.97
Exon sequences
Seq C1 exon
GTGGGAGAACCTGCTGTGCACATCCAAGGGCAGGAGCCGCTGACGGCATCCATGCTTGCAGCAGCCCCTCCGCAGGAGCAGAAGCAAATGATAG
Seq A exon
GTGGGTGTCCAGGCTGCCTGAGATCCTCCTGCCTGGGCATGCATGGGCAAGTGGACTTGTGTATGTTAAGGAAGGCATAGATGACAGGAGAAGCTCTAAGCCTGTGTTGGATTTCTCTAATATTATGTTGCTTTAAAAAGGAGGGGAAAAAAAAAAGTCTAGGCTGTGTTGGAAGGATATGGAACGAGCAACCTCCTCTCTGTCTGCATGCACTGCCTGGCAGTGGGGTGGGCTCTGCAGGAGAGGCACAGCTCCATCCTGCCTTGTGCTGCCCTCTGCAGCTGTCTGACTTCACCTGACAGCTTCTCTCCATGTGGAAAACCCCCCCTGGGCTCAGCAAAGGGCTGGGAGCAGAGCAGTTTGAGGAAGGAAGAGGGGAGGCATAGAGTTGGGAGTGCAGGGGGACTTCCACTGACATCTTCCCTGGTGCTTCGGGCAG
Seq C2 exon
GTGAGCGGCTCTACCCCCTGATCCATGCAATGCACGCCTCACTGGCTGGCAAGATCACAGGCATGCTGCTGGAGATCGACAATTCAGAGCTGCTGCTTCTGCTGGAGTCCCCTGAATCCTTGCACTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004123:ENSGALT00000006565:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.781 A=NA C2=0.023
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(27.8=62.5)
A:
NA
C2:
PF0065813=PABP=FE(59.7=100)
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:
GGAGAACCTGCTGTGCACATC
R:
CTTGGAGTGCAAGGATTCAGGG
Band lengths:
222-661
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]