GgaINT1020563 @ galGal4
Intron Retention
Gene
ENSGALG00000014450 | PABPC1
Description
polyadenylate-binding protein 1 [Source:RefSeq peptide;Acc:NP_001026768]
Coordinates
chr2:128383384-128383801:-
Coord C1 exon
chr2:128383607-128383801
Coord A exon
chr2:128383500-128383606
Coord C2 exon
chr2:128383384-128383499
Length
107 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGT
5' ss Score
8.54
3' ss Seq
ACAAAGTTTTTCTTTAATAGGTG
3' ss Score
7.42
Exon sequences
Seq C1 exon
GCTGAACGAGCTTTGGATACTATGAATTTTGATGTCATCAAAGGCAAACCGGTGCGCATTATGTGGTCCCAGCGTGATCCATCTCTACGCAAAAGCGGCGTTGGAAACATCTTCATCAAAAACTTGGACAAATCAATTGATAACAAAGCTTTGTATGACACATTTTCTGCTTTTGGAAACATCCTTTCTTGTAAG
Seq A exon
GTTAGTGACAAGTTATGGCTGCGTTTAATGATTAGACATTAAAAAAAAGAATTCAAATTATGCGGGAAACATTCCATGGTTACTACGACAAAGTTTTTCTTTAATAG
Seq C2 exon
GTGGTATGTGATGAAAATGGATCCAAGGGTTATGGATTTGTACATTTTGAGACACAAGAAGCTGCAGAAAGAGCTATTGAAAAAATGAATGGTATGCTGCTTAATGACCGCAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014450:ENSGALT00000023333:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(40.6=43.1)
A:
NA
C2:
PF0007617=RRM_1=FE(55.1=100)
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:
CAGCGTGATCCATCTCTACGC
R:
ACTTTGCGGTCATTAAGCAGC
Band lengths:
242-349
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]