GgaINT0010606 @ galGal3
Intron Retention
Gene
ENSGALG00000004123 | PABPC1L
Description
NA
Coordinates
chr20:5203119-5204275:-
Coord C1 exon
chr20:5204082-5204275
Coord A exon
chr20:5203235-5204081
Coord C2 exon
chr20:5203119-5203234
Length
847 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
CTCCTGCTCTGCTTTTGTAGGTG
3' ss Score
10.72
Exon sequences
Seq C1 exon
CTGAGCGAGCCCTGGACACCATGAACTTTGAAGTGATCAAGGGCCGACCTGTCCGAATCATGTGGTCCCAGCGAGACCCTGGGCTCAGGAAGTCAGGGGTTGGAAACGTCTTTATCAAGAACCTGGATGACTCCATTGACAATAAAGCCCTGTACGACACATTCTCAGCCTTTGGGAACATCCTGTCCTGCAAG
Seq A exon
GTACATCCCCGTGGCTGCACTGCTGCGGAGGGGAGCTGCTGTATGCAGAGCTTCCCCACACTGTTTCAAAGTTTCCTTTGACTTCCCACCCTTTTCCTGGGTAGAAGCATTCTGTGTTTCCTATGGGGGTGGGGAAGGCTTTTCTTCCCCCACTTTCCCTTTATTTCTTCCTCCTGATCCCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGATTCTGATCCCTGGCCTGCTGCCTGCAAACACCCGAACACAGCTCTGCGTCCTTACTCGTGTGCAAGGATGAAGAAAACCAGCGTCTGTGGATCTTCTTTCCTCCTGCTCTGCTTTTGTAG
Seq C2 exon
GTGGTCTGTGATGAAAATGGATCCCGTGGCCATGGCTTTGTTCATTTTGAGACTCAAGAGGCAGCAACTCGGGCCATCCAGACCATGAATGGGATGCTCCTCAATGACCGCAAGGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004123:ENSGALT00000006565:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.026
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(25.4=27.7),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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGAGCGAGCCCTGGACA
R:
ACCTTGCGGTCATTGAGGAG
Band lengths:
310-1157
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]