GgaINT0036342 @ galGal3
Intron Retention
Gene
ENSGALG00000002725 | UAP1
Description
NA
Coordinates
chr8:3844072-3844618:-
Coord C1 exon
chr8:3844413-3844618
Coord A exon
chr8:3844248-3844412
Coord C2 exon
chr8:3844072-3844247
Length
165 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
GCCCCTGTGTTCCCCTGCAGGTA
3' ss Score
13.13
Exon sequences
Seq C1 exon
GGGCTGGCGGAGATCGCGGCGGGCCGCGTGGGCGCGCTGCTGCTGGCCGGAGGGCAGGGAACCCGGCTGGGCGTCCCCTACCCCAAGGGCATGTGCGACGTGGGGCTGCCCTCCCGAAAGAGCCTCTTCCACCTGCAGGCCCAGCGCCTGCGGCGGCTGCAGCAGCTGGCGGAGGAGCGGCACGGCACGGCGTGCAGCATCCCCTG
Seq A exon
GTGAGCGGGCCGGGGCTCTGCGGCTCGGCGCCTTCCCTGCTGCGCGGTGCCGCCGGCTGTCACCGTGCGGGTGACGCCCGCCGTTGGCTTGGCCGAGAGGAGGCCCCGGTGGGCTCTGTAAGCCCCTCGCGGGGTGAGGATGCCAGCCCCTGTGTTCCCCTGCAG
Seq C2 exon
GTACATCATGACGAGCGGGCGGACCGTGGAATCCACCAAGGAGTTCTTCCAGAAGCACCGCTACTTCGGCCTGAAGAAGGAGAACGTCATCTTCTTCCAGCAGGGCATGCTGCCCGCCCTGGGCTTCGACGGGAAGATCCTGCTGGAGGAGAAGGGCAAGATCGCCATGGCGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002725:ENSGALT00000004299:1
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:
PF0170413=UDPGP=PU(17.9=98.6)
A:
NA
C2:
PF0170413=UDPGP=FE(15.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAAGAGCCTCTTCCACCTGC
R:
CGATCTTGCCCTTCTCCTCCA
Band lengths:
255-420
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]