BtaINT0128838 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020780 | SBNO2
Description
Bos taurus strawberry notch homolog 2 (Drosophila) (SBNO2), mRNA. [Source:RefSeq mRNA;Acc:NM_001077911]
Coordinates
chr7:45219040-45219372:-
Coord C1 exon
chr7:45219282-45219372
Coord A exon
chr7:45219184-45219281
Coord C2 exon
chr7:45219040-45219183
Length
98 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGG
5' ss Score
5.87
3' ss Seq
ATGTCCGCCCTCTCCCCCAGATC
3' ss Score
11.51
Exon sequences
Seq C1 exon
GTTCAGCGTCTCCAATGATCTCAAGTACGACGCAGAGCGCGACCTCCGGGACATCGCCGCCCCCGGCATCGCGGTGCACGCACTGAGCAAG
Seq A exon
GTGGGGTGGCCGCAGCCCCAAACCTGGTGTGGGTCGGGGTCACGGAGCCCAGCTCTGGCCAAGCCACCTCATGCACAGATGTCCGCCCTCTCCCCCAG
Seq C2 exon
ATCAAGTACGGCGACAACACTACCTCAGAGGGCGTCCTCTTCGCCACCTACTCTGCCCTGATTGGTGAGAGCCAGGCGGGTGGGCAGCACCGCACGCGCATCCGGCAGATCCTGGAGTGGTGCGGGGAGGCCTTCGATGGCGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020780:ENSBTAT00000027693:10
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(10.2=100)
A:
NA
C2:
PF138721=AAA_34=FE(15.9=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:
GTTCAGCGTCTCCAATGATCTCA
R:
GCCTGGCTCTCACCAATCAG
Band lengths:
168-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]