DreINT0018588 @ danRer10
Intron Retention
Gene
ENSDARG00000016188 | SBNO2 (1 of 2)
Description
strawberry notch homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:HGNC:29158]
Coordinates
chr22:17672675-17672931:-
Coord C1 exon
chr22:17672860-17672931
Coord A exon
chr22:17672784-17672859
Coord C2 exon
chr22:17672675-17672783
Length
76 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
GTTTTGGCTGTTCCTCACAGTAC
3' ss Score
5.75
Exon sequences
Seq C1 exon
GGAGCTTTGACTCATGGTGACAGGAGAGCCACAGAGTCTAGAGACCTGAGCAAATACAACTTTGAAAATAAA
Seq A exon
GTAAGTAACTGTTTCACATAACACAGAGTAAAACACATGTCATTGACTAACACATTGTTTTGGCTGTTCCTCACAG
Seq C2 exon
TACGGTACCAAAGCTCTTGATAAGATCACCAAAACCATCCTTGGTCAAACTGAAAGCAAGGTACCTCCTCCAAAGGACTATCCTGGTGGAGAAGCCATGTTTTTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016188:ENSDART00000137984:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.125 A=NA C2=0.324
Domain overlap (PFAM):
C1:
PF138711=Helicase_C_4=FE(8.3=100)
A:
NA
C2:
PF138711=Helicase_C_4=FE(12.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGCTTTGACTCATGGTGAC
R:
TGGCTTCTCCACCAGGATAGT
Band lengths:
169-245
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]