GgaINT0145723 @ galGal4
Intron Retention
Gene
ENSGALG00000002672 | SBNO2
Description
strawberry notch homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:HGNC:29158]
Coordinates
chr28:2875290-2876038:-
Coord C1 exon
chr28:2875905-2876038
Coord A exon
chr28:2875381-2875904
Coord C2 exon
chr28:2875290-2875380
Length
524 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
GCCCACGTCTTGCTTTGCAGGTT
3' ss Score
10.18
Exon sequences
Seq C1 exon
CAACATGAAGTTTTATTACCCAATGGGCAGCGAGCTGGCTTCCTCATCGGGGACGGTGCTGGAGTTGGAAAGGGCAGGACAGTTGCGGGCATCATCTTTGAAAATTATCTTAAAGGGAGAAAAAAAGCTCTTTG
Seq A exon
GTAAGTTGGGTTTTTTTTCCCCTCTTTTCCCGTAAGACCTCGGAGTTAGTGTGAATCTGGGAGTAAGGAATTCCTTAATGCTGATGTTGGCTTTGTAGTTGACTCATGTTGTGGCCTTGGGTAAGTGTTTTCCACCTCTTTGTGCCTGTTTGCTCTCTGTGAAATGGGAATATTTCCCCTGCAGCGGTGATGGAGAATGAATCACTCTGAAACGGCAAATTGTGTACTCCTCAGAGTGCAGTGTGAAGCCTCTTCCTACTCCTCTGAAGTCGGTGGAGGGATATTCATGGACTTCCCAGGTGCAGACTTGAGCCCCTACAGTATGGGGCTTTACTGCAGAATAGACACAGCTTGTCATAAGTGCCAGACCAGAGTCTGCTGTAGGATCTTACGTTGAGGTGTGTGGGCAGTGGGAAATGTGACAGTTTTATACACCTACAATTGCTTTAGTCAGAGCTGTTAATCACTGTGCGTGCCCCGACTCTCTCCTTAGGAGATAACCAGGCCCACGTCTTGCTTTGCAG
Seq C2 exon
GTTCAGCGTCTCCAATGATCTCAAGTATGATGCTGAGAGAGACCTGAAGGACATTGAAGCCTCCCACATTCCTGTGCATGCTTTGAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002672:ENSGALT00000004211:6
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=0.000
Domain overlap (PFAM):
C1:
PF138721=AAA_34=FE(14.8=100)
A:
NA
C2:
PF138721=AAA_34=FE(10.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAACATGAAGTTTTATTACCCAATGG
R:
ATTCAAAGCATGCACAGGAATGTG
Band lengths:
222-746
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]