DreINT0018611 @ danRer10
Intron Retention
Gene
ENSDARG00000098801 | SBNO2 (2 of 2)
Description
strawberry notch homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:HGNC:29158]
Coordinates
chr2:57081146-57081713:-
Coord C1 exon
chr2:57081531-57081713
Coord A exon
chr2:57081268-57081530
Coord C2 exon
chr2:57081146-57081267
Length
263 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
TCATCCTGTGTGTGTTTCAGCTA
3' ss Score
10.46
Exon sequences
Seq C1 exon
GAAAACCCAGAGGCCGGCCTTCAAAGTTTCCTAAGCAGCGTGTGGAAGTGGGCGGAGTTATTAAAATCAGCGATGACTCAGACTCTGACTCTGACGAGTTTGACAGCGAATCAAACTCCTCCCCCGAATCACTACAGGACAATGATGATGTGATTTTCGTCAACCACATCAACGGGCCTGCTG
Seq A exon
GTAGGTGGATTTAACACACAATCACAGATCTGTCATTCAGCGTTCATACAGTCATTGGAAAATCTTGAAAAGTCATGAAATTCTGACATGGCATTTTCCAGGCCTGGAAAAGTTTTGAAATAATTATCCTGTGCTCCCCTGTTCATTCAGTTATTAAAGCAGTGCAGATGCAGCTTAATAGATGACTGCTCATTTCAGTCTAGACGCAGCGATTAATATCTTTATCCATACCCGATCTGGAAGTCATCCTGTGTGTGTTTCAG
Seq C2 exon
CTAAACTGGAGGAGCTGAAGCAGAGGCTGCTGCATAGAATAGCGGAGCTGGGAAAGGAGTTGCCGCTGAACACTCTGGATGAGCTGATCGACCGATTCGGAGGACCAGAGAAAGTGTCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000098801:ENSDART00000159719:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.694 A=NA C2=0.220
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138711=Helicase_C_4=PU(6.1=41.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCGGCCTTCAAAGTTTCCTA
R:
TCCGACACTTTCTCTGGTCCT
Band lengths:
292-555
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]