BtaINT0128824 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020505 | SBNO1
Description
strawberry notch homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:HGNC:22973]
Coordinates
chr17:54528252-54528577:+
Coord C1 exon
chr17:54528252-54528398
Coord A exon
chr17:54528399-54528482
Coord C2 exon
chr17:54528483-54528577
Length
84 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
GTTGCTTTTTCTTATTCAAGATC
3' ss Score
5.41
Exon sequences
Seq C1 exon
ATTATAACAACATAGGAAAATTCTTAAACAGAATTTTGGGCATGGAAGTGCATCAACAGAATGCACTATTTCAGTATTTCGCAGACACACTTACTGCAGTCGTTCAAAATGCCAAAAAAAATGGAAGATACGATATGGGAATCTTAG
Seq A exon
GTAAGTTGGGAAGTTTTTAAAATGTCATGTGTATTCCTGATGAAAAATTATTTTATACTTATATGTTGCTTTTTCTTATTCAAG
Seq C2 exon
ATCTTGGTTCTGGGGATGAAAAAGTGAGGAAAAGTGATGTTAAGAAGTTTCTGACTCCAGGATATTCAACATCTGGCCATGTAGAATTATACACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020505:ENSBTAT00000027325:26
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=0.000
Domain overlap (PFAM):
C1:
PF138711=Helicase_C_4=FE(17.7=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:
GGAAGTGCATCAACAGAATGCAC
R:
TGGCCAGATGTTGAATATCCTGG
Band lengths:
183-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development