DreINT0018591 @ danRer10
Intron Retention
Gene
ENSDARG00000016188 | SBNO2 (1 of 2)
Description
strawberry notch homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:HGNC:29158]
Coordinates
chr22:17672113-17672436:-
Coord C1 exon
chr22:17672293-17672436
Coord A exon
chr22:17672208-17672292
Coord C2 exon
chr22:17672113-17672207
Length
85 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
AAGTATCTGCTTTCTTTTAGATC
3' ss Score
8.7
Exon sequences
Seq C1 exon
ACTGCAATATCACCAAGTTCCTCAACCGGATACTGGGTCTTGAGGTGCACAAACAGAACTCCCTCTTCCAGTACTTCACGGACAATTTCGACTACTTGATTGAAATGGACAAAAAAGTGGGCAATTATGATCTGGGAATACTGG
Seq A exon
GTAAGCAGAGCTTCTTCTGGTGGTGTGGTACTTTTAACTTGGATCAATAGTTTTACGTGACAGCCAAGTATCTGCTTTCTTTTAG
Seq C2 exon
ATCTGGCTCCAGGTAATGATCAGATCTATGAAGAGACGCAGGAAAAGTTTCTGACAGCGGGAAACCCTCAAGATGGTCAAGTTGTCCTGTATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016188:ENSDART00000137984:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.156
Domain overlap (PFAM):
C1:
PF138711=Helicase_C_4=FE(17.3=100)
A:
NA
C2:
PF138711=Helicase_C_4=PD(0.1=0.0)
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:
GGGTCTTGAGGTGCACAAACA
R:
GGTTTCCCGCTGTCAGAAACT
Band lengths:
176-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]