HsaINT0178675 @ hg19
Intron Retention
Gene
ENSG00000136878 | USP20
Description
ubiquitin specific peptidase 20 [Source:HGNC Symbol;Acc:12619]
Coordinates
chr9:132631141-132631704:+
Coord C1 exon
chr9:132631141-132631281
Coord A exon
chr9:132631282-132631588
Coord C2 exon
chr9:132631589-132631704
Length
307 bp
Sequences
Splice sites
5' ss Seq
AAGGTTCGG
5' ss Score
5.96
3' ss Seq
GTCCTGTGCTGTGTCCCCAGCCC
3' ss Score
8.56
Exon sequences
Seq C1 exon
AGCCGGACAATGATGCTCACCTACGCAGCTCCTCTCGCCCCTGCAGCCCCGTCCACCACCACGAGGGCCATGCCAAGCTGTCTAGCAGCCCCCCTCGTGCAAGCCCCGTGAGGATGGCACCGTCGTACGTGCTCAAGAAAG
Seq A exon
GTTCGGGGGGCACGGGAGGGTGGGTCAGCTTGAGGCTGGGAGTACAGATTACGCCCGTAGCTGCCTTTCTCATGGCCCCCTGTGGCGGAGGGCCGGGCTATGGGCTCCTCTCAGGTACACCCCTGAGACACCAGTGTGGGAGCCACGTTTTGCAGAGGATGACACAGAGGCATGAGATGGTGAATTGCTTACCCAGTCATGTGACTCACGGATGTCACTCCACATCCTGTCAAAGGAAGCCGCAGGGCCCGCACCTCGCCCCGGCCAGGCAGGTGGAGGCTGGGCTAGTCCTGTGCTGTGTCCCCAG
Seq C2 exon
CCCAGGTATTGAGTGCTGGCAGCCGGAGGCGGAAGGAGCAGCGCTACCGCAGCGTCATCTCAGACATCTTTGACGGCTCCATTCTCAGCCTTGTGCAGTGTCTCACCTGTGACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136878-USP20:NM_001110303:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.833 A=NA C2=0.051
Domain overlap (PFAM):
C1:
PF0044324=UCH=FE(8.7=100)
A:
NA
C2:
PF0044324=UCH=FE(7.1=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:
AGCCGGACAATGATGCTCAC
R:
GTCACAGGTGAGACACTGCAC
Band lengths:
254-561
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)