GgaINT1020573 @ galGal4
Intron Retention
Gene
ENSGALG00000014450 | PABPC1
Description
polyadenylate-binding protein 1 [Source:RefSeq peptide;Acc:NP_001026768]
Coordinates
chr2:128378359-128378912:-
Coord C1 exon
chr2:128378640-128378912
Coord A exon
chr2:128378453-128378639
Coord C2 exon
chr2:128378359-128378452
Length
187 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
AATGTTTTTGCATCTGACAGACT
3' ss Score
5.66
Exon sequences
Seq C1 exon
GTCATGATGGAAGGTGGACGCAGCAAAGGATTTGGGTTTGTCTGCTTTTCGTCACCAGAAGAAGCCACCAAAGCTGTCACAGAGATGAATGGTAGAATTGTGGCTACTAAACCACTGTATGTAGCTCTAGCCCAGCGTAAAGAAGAGCGCCAAGCTCATCTCACCAACCAGTATATGCAGAGAATGGCGAGTGTAAGAGCAGTCCCTAATCCAGTAATCAACCCCTACCAACCAGCACCTCCTTCAGGTTACTTCATGGCAGCTATCCCACAG
Seq A exon
GTATGTATAAAGCTGAGTAACTGAATGCTTAGTACTATGTATATAATTTGTTTAGATTTAAAAGTAAATAAAACAATTAGCATTTATTCATAATTTCAGCATTGTAATTTCATAGCAGAAAAGTGATTCACTGCTCAGCACGCCCTCTGAAGATAACAGGGTAACATAATGTTTTTGCATCTGACAG
Seq C2 exon
ACTCAGAACCGTGCTGCATACTATCCTACTAATCAACTTGCTCAACTTGCTAGACCTAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014450:ENSGALT00000023333:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.302 A=NA C2=0.719
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=42.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCAGAAGAAGCCACCAAAGC
R:
AGTATGCAGCACGGTTCTGAG
Band lengths:
242-429
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]