DreINT0172498 @ danRer10
Intron Retention
Gene
ENSDARG00000027501 | usp20
Description
ubiquitin specific peptidase 20 [Source:ZFIN;Acc:ZDB-GENE-040426-1219]
Coordinates
chr5:32700852-32701088:+
Coord C1 exon
chr5:32700852-32700950
Coord A exon
chr5:32700951-32701034
Coord C2 exon
chr5:32701035-32701088
Length
84 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGA
5' ss Score
6.12
3' ss Seq
ATGTTTTTTTTTTTTTCAAGGGC
3' ss Score
9.46
Exon sequences
Seq C1 exon
AGTGAGAAGAAAATCAGGATGACTGACAGCGGGGATCTTTGTCCTCACTTGGACTCGATTGGTGAAGTTACTAAAGAAGAACTGATTCAGAAATCAAAG
Seq A exon
GTTAGAATTAATTTAGCTGATGTACAGGACTTAATATAATGAGTGCAGTGGATTGAATATTGTTATGTTTTTTTTTTTTTCAAG
Seq C2 exon
GGCACGTGTCAGTCATGTGGAGTAGGTGGACCAAATCTCTGGGCATGTCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000027501:ENSDART00000006021:2
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:
NO
A:
NA
C2:
PF0214814=zf-UBP=PU(22.7=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGAGAAGAAAATCAGGATGACT
R:
ATGCCCAGAGATTTGGTCCAC
Band lengths:
145-229
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]