GgaINT1020564 @ galGal4
Intron Retention
Gene
ENSGALG00000014450 | PABPC1
Description
polyadenylate-binding protein 1 [Source:RefSeq peptide;Acc:NP_001026768]
Coordinates
chr2:128376684-128377360:-
Coord C1 exon
chr2:128377206-128377360
Coord A exon
chr2:128376769-128377205
Coord C2 exon
chr2:128376684-128376768
Length
437 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
GGTGTAAAATTAATTTGCAGCCT
3' ss Score
4.32
Exon sequences
Seq C1 exon
CTAATACATCAACACAAACAATGGGTCCACGTCCTGCAGCAGCAGCTACTGCAGCTACTCCTGCTGTACGCACAGTACCACAGTACAAATATGCTGCAGGTGTTCGTAATCCTCAGCAGCATCTTAATACACAGCCACAGGTTGCTATGCAGCAG
Seq A exon
GTATGTAATTTTAGGTACTGCTCATGCTTTTGCTGGGTTTTCTGCAGATTAAGGGTGGAGATGTGTGTGATTAAGAGTTTCCTTTGTTTATCTAGAATTCAGGCTTTGCATTATGGCACCAGTAGAGTTTGGGGCTTTAAGTATGTTTCAAGTTCCCCTGGGATGGGATGGGATCCTATCTTACTTTGTTTTCTGATTTGATACCTTAACCTAAATTTTCCTTGTGATTGCTCCACAATGGAACAGTTGATGCTTATCTCCAGCATCACTCAGTCTGAACCAGCTCTATTCGATTAAATTGACTTGGATGTAATGTATTCCAGGTTTCTGACAGTGTAGGCATTGTTTATGCTGAGTTGTGTAACGTTGGATATTTGAAGCTGCAACTAATTATAAGCTGGAATTTAATCTCTAAATGGTGTAAAATTAATTTGCAG
Seq C2 exon
CCTGCTGTCCATGTGCAAGGCCAGGAACCCTTGACTGCTTCCATGTTGGCTTCTGCCCCTCCACAAGAACAAAAGCAGATGTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014450:ENSGALT00000023333:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.885 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(27.8=69.0)
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:
ACACAAACAATGGGTCCACGT
R:
CTGCTTTTGTTCTTGTGGAGGG
Band lengths:
222-659
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]