GgaINT0124249 @ galGal4
Intron Retention
Gene
ENSGALG00000004142 | USP20
Description
ubiquitin specific peptidase 20 [Source:HGNC Symbol;Acc:HGNC:12619]
Coordinates
chr17:5720127-5720860:+
Coord C1 exon
chr17:5720127-5720239
Coord A exon
chr17:5720240-5720687
Coord C2 exon
chr17:5720688-5720860
Length
448 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
TTCCTCTTGGATATTTCCAGGTT
3' ss Score
7.01
Exon sequences
Seq C1 exon
CCCAGATGCAGGCTTCTGGGAAAAAGAAGAAAGAACTTCGTTATCGCAGTGTGATCTCTGATATCTTTGATGGCTCCATCCTCAGCCTGGTGCAGTGCCTCACCTGTGACAGA
Seq A exon
GTGAGTGTCCTGATAGCTGTTGGTCAATGAGCAGTCTTCTGTAGACCTCATAGACCTCTTTTTTTGTTGGTTTTTTGGTTTTTTTTTTTTGGCAATGAAGCTTTCTGTTTCCATGCTGTGGGATGCAGCAGGCCTGCTAAAATCTTGGCAGGTGGGATGTGTTTGAGACCTGCCATGCCAAGAAATTTTCAGCCTCCGTAGTGATGTTTGCTTATCTGTGCTACTGAGTTGGTCTAGCACTGTCACATTCACATCAGAAAACAAATTCCAACTCTGCAAAAAGATGGTGAAAGTCCTCCTGCTGACAGTAGGTAAGAAGAACTAGCCTGAGCAAGTTGCTGTTACTGCCAGGTCAGGTTTCTGCAGTGATTAAAAAGTGATGGAAGTCAGGTCCTGGCTTCATTACGTGCACAGGAAACCCAGGCTTTTTCCTCTTGGATATTTCCAG
Seq C2 exon
GTTTCTACAACAGTGGAGACATTCCAAGACCTGTCACTCCCAATCCCAGGGAAGGAGGACCTGGCCAAGCTGCACTCTGCCATCTACCAAACAGTGCCAGCTAAGACAGGGGCATGTGGGGACAACTATGCCTCGCAAGGCTGGATTGCTTTCATCATGGAGTATATCCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004142:ENSGALT00000006585:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.026 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0044324=UCH=FE(6.9=100)
A:
NA
C2:
PF0044324=UCH=FE(10.7=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:
CCCAGATGCAGGCTTCTG
R:
CTCCGGATATACTCCATGATGAAAGC
Band lengths:
286-734
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]