GgaINT0010609 @ galGal3
Intron Retention
Gene
ENSGALG00000004123 | PABPC1L
Description
NA
Coordinates
chr20:5201105-5201633:-
Coord C1 exon
chr20:5201539-5201633
Coord A exon
chr20:5201243-5201538
Coord C2 exon
chr20:5201105-5201242
Length
296 bp
Sequences
Splice sites
5' ss Seq
AAGGCAAGC
5' ss Score
2.46
3' ss Seq
GAGCTGCGTTCTGCCTGCAGGCC
3' ss Score
9.64
Exon sequences
Seq C1 exon
GAAAGACACTGAGTGTCAAAGTGATGATGGACCACACCGGCCGCTCCAAGGGCTTTGGGTTCGTGAACTTTGAGAAACACGAAGAAGCCCAGAAG
Seq A exon
GCAAGCAGCTCCTTGCTGTGGAGCTGGTGGGCAGCCTGGCTGCCTGCTGCTGGCTCAGGTCACCTGCTGAGATCTCCCCTGTCCTGGAACGGGAGCTTGATGTCCCCGCTGGCCATGGTGTCACATCACTGTGGGCAATGGGAATGGGCAACACCTGTCCAGGCCAGCCTTTTGGCCAGGGTGGGGGCGGACTTTTATGAGGGCACAGCTCCTGCCCTGCGCTCAGCTCTGCTTGTGGTGGGGTTGGGGCGGTGGGGAAGGGTTCTGCTGGGCTCAGAGCTGCGTTCTGCCTGCAG
Seq C2 exon
GCCGTGGCTGACATGAACGGAAAGGAGATCAACGGGCGGATGGTGTACGTGGGCCGGGCGCAGAAGCGGCTGGAGAGGCAGAGTGAGCTGAAAAGGAAATTTGAGCAGATGAAGCAGGAGCGAGTGAGCAGGTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004123:ENSGALT00000006565:5
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=0.196
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(44.3=100),PF073187=DUF1464=FE(31.0=100)
A:
NA
C2:
PF0007617=RRM_1=PD(21.4=32.6),PF073187=DUF1464=FE(45.0=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:
ACACTGAGTGTCAAAGTGATGATGG
R:
CTGGTACCTGCTCACTCGCTC
Band lengths:
228-524
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]