GgaINT0010615 @ galGal3
Intron Retention
Gene
ENSGALG00000004123 | PABPC1L
Description
NA
Coordinates
chr20:5197714-5198224:-
Coord C1 exon
chr20:5198091-5198224
Coord A exon
chr20:5197808-5198090
Coord C2 exon
chr20:5197714-5197807
Length
283 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTG
5' ss Score
6.13
3' ss Seq
CTCTGTATTTCTTCACCCAGGTG
3' ss Score
8.95
Exon sequences
Seq C1 exon
CCAACATAGGGACGCAGACGATCAGTGCCCGGGTGCCCTCCTCACCCACCCTGCGAGGCGCCCCGCAGTACAAGTACTCCCTGGCTGTGAGGAACATCCAGCCGATGGGCAGTGTGCCACCCGGGGCTCAGCAG
Seq A exon
GTAGTGCCCAGTGGGGTATCCCATGGTTTTGGTCCTAACTGTTGTGATGGAATCCCTTCCTGAGCTCCAGGTGCTCATCCTGGAGCAGTGTAGATGTGATGCCTGGCTCTGGTTTTCCGCAGAAGCTTGTACTGGGATACAAGCAGGCAGTGCCAGAGCTTGCACTGGTGGCTCTGGAGGGCAAAATGCCCCACTGCATCCAAGGGCCAGCACTGTTCCTGTATGCCAACTCGCTCTTTGCTTCCAGCCTGACTGTTGCTCTTCTCTGTATTTCTTCACCCAG
Seq C2 exon
GTGGGAGAACCTGCTGTGCACATCCAAGGGCAGGAGCCGCTGACGGCATCCATGCTTGCAGCAGCCCCTCCGCAGGAGCAGAAGCAAATGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004123:ENSGALT00000006565:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.600 A=NA C2=0.781
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(27.8=62.5)
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:
CCAACATAGGGACGCAGACGA
R:
CTATCATTTGCTTCTGCTCCTGC
Band lengths:
228-511
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]