GgaINT0124244 @ galGal4
Intron Retention
Gene
ENSGALG00000004142 | USP20
Description
ubiquitin specific peptidase 20 [Source:HGNC Symbol;Acc:HGNC:12619]
Coordinates
chr17:5714378-5715134:+
Coord C1 exon
chr17:5714378-5714447
Coord A exon
chr17:5714448-5715020
Coord C2 exon
chr17:5715021-5715134
Length
573 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGC
5' ss Score
6.99
3' ss Seq
TTCTTCTTGTTCTCTTGTAGCCC
3' ss Score
10.67
Exon sequences
Seq C1 exon
GCCTTACTGGAATGAAAAATCTTGGGAACTCCTGCTACATGAATGCAGCACTTCAGGCTCTCTCTAACTG
Seq A exon
GTAGGCACTAGGGCCTTTAGTAGAGTCTTTTACTAGACATCATTACATATCAGCAGTGGCACCTCTGATCTGGCACCTTCCTTAGTTGTGCAAGGATAAACCAGCCAGACTAGCTACAGAAAAAGGAATATGAAAAGTTAGTGTTTAGGAGAACAGAAGTTCTGCAGTAGGAAAATGGGTGAATAGCCAACTTGTGGCTGTAAGACTTGTCTTTAGATGAATGCTGGAAGTAAAACTCCTTTCCACCATGACAGAAACGTATCTGCCACACAACAAAATGTGCAATCTTTCTGCTTTCCACGGTGGTATCATTCCAACCACTCACACTGTAGGATTTGCCATTCTGCTGACAACTAGTTTCAGGATCTCTGTGCTGGGAAGAGATTCAGATCAGCCTTCTTTGTTCGTTTCTAGGCAGAAGTCAAGTTTGCATCTAGAATCACTTCTTCCCTTGATTTAAAAGCACTATCTTAAGCATGTTTTCAGAAAGGGATGTGTTTAAGTTTTGATAAATCCTTAAATAGAGGCAGAGAAGAAATTTCTATGCTCTGAATTCTTCTTGTTCTCTTGTAG
Seq C2 exon
CCCACCTCTCACACAGTTTTTTCTGGAATGTGGTGGTCTGGTCCGTACAGATAAGAAACCAGCACTATGCAAAAGTTACCAGAAGCTGGTGTCTGAGGTTTGGCATAAGAAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004142:ENSGALT00000006585:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.042 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0044324=UCH=PU(24.7=91.7)
A:
NA
C2:
PF0044324=UCH=FE(42.7=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:
GCCTTACTGGAATGAAAAATCTTGGG
R:
CGTTTCTTATGCCAAACCTCAGAC
Band lengths:
184-757
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]