BtaINT0128833 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020505 | SBNO1
Description
strawberry notch homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:HGNC:22973]
Coordinates
chr17:54505855-54507474:+
Coord C1 exon
chr17:54505855-54505951
Coord A exon
chr17:54505952-54507313
Coord C2 exon
chr17:54507314-54507474
Length
1362 bp
Sequences
Splice sites
5' ss Seq
AATGTATGT
5' ss Score
5.87
3' ss Seq
ATTTTTAAACCTTTGTTTAGTAA
3' ss Score
3.92
Exon sequences
Seq C1 exon
AAGGTCCCTGTTGTGAAAGAGGAAGATGAACCAGAAGAAGAAGACGAAGAAGAAATGGGTCATGCGGAAACCTATGCAGAGTATATGCCAATAAAAT
Seq A exon
GTATGTCTTTGAGATTTGTTAAAATAATGAAAAACCTCTGGGTTCCTTTCAAACTTAAAAACTTTTCCCCACACATTGTTACCTATTAGGATCTGTCCATGTTGGGTACCTCAGGATTTGATAAGTATGAGCTGTGTATGAATATGTTTTAAAATAGCTACATGAAAATTCTACTGTGAGTTTTAATTTCCCTACACAAATTTAGAACTTTGTTTTGGAATGAAGTCTTAAAACCAAGAGTAAAAAAGCTTATTCCTTTCAAGTTAATTTTGCTCATATCAGCGGTGATTATAAAATCAGAGTAAATTACAGAGATGTAAACATATATCTTAGCGTTATAGTTTATACAGCTTATCTAAAACAAGCTATAAAAGCATGGGAATCTTAAAATAAAATGTGCTATTTGAATTCAGTGGCTTAAATTAACACCATTTCTTCCTCTTTTCCCCACAAGGACCGTGATTCAGTTTTTGTTTTGTTTTTTTTGAAGTGGCCAGTATATTAAGTTGAAAATTAGTAATTTTTAGTTTATATATAAATTTTTTCACGTTTTCATTTTCTGAGGGTAATAAAATGGGAAAATGTATGGCTAGAATTTGTTTCTCATACACTCTGGGTTTCTATAAAACGTCACTAATAAGACCACTTAAACTAAAAATCTGTTTACCAACTGTATATGGATTCTAGTTCCCTACTTTGTAGATCATTTAAAATGAACGTAACCTAGGAGTGTGCTCTGCTACTGTGGAGAACCTCGTGGTATGAATTGAGATTGTATTTTCCTAGATCTTTTTAATCAGCGAGTCTCTTTCTATAAATTTATTTTAACTGGAGGATAATTACTTTACAATGTTGTGTTGGTTTCTGCCGTATAACATGAATCAGCCATGCTATGCTTAATCGCTCAGTCATCTCCGATTCTTTGCAGCCGTATGGACTGTAGCCCACCAGGCCCCTCTGTTCATGGGGATTCTCCAGGCAAGAATACTGGAGTGGGTTGCCATCCCCTCCTCCAGGGGTTCTTCCCAACTCAGGGATCGAACCCAGGTCTCCTGCATCGCAGGTGGTTGCTTTACTGTGTGAGCCACCAGGGAAGCCCGAATCAGCCATGTCTCTATGAATCCCCTCCCTGTTGAGCCTCCCCCAACCCTCACAAGTCTCTGTTTAAACCATAGGTAGTTGGTAATTAGATCACATTAGTTAAGTTTAACAGTACTTTACATCATTCGGTGACTTTATATAGGATCCCAGGGTTACTTACATTTCTCTGTCAGAGGAGAAATGCTATAATATTTTATGATAAGAGTGGAAGTGTTATTACTCAGAATAATTAAAATGAAGTATTTTTAAACCTTTGTTTAG
Seq C2 exon
TAAAAATTGGCCTACGTCACCCAGATGCCGTAGTTGAGACTAGTTCTTTATCCAGTGTTACTCCTCCTGATGTTTGGTACAAGACATCTATTTCTGAAGAAACCATTGATAATGGCTGGTTATCAGCATTACAGCTTGAAGCAATTACTTATGCAGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020505:ENSBTAT00000027325:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.727 A=NA C2=0.037
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138721=AAA_34=PU(16.2=92.6)
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:
AGGTCCCTGTTGTGAAAGAGGA
R:
CTGGGCTGCATAAGTAATTGCT
Band lengths:
257-1619
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development