BtaINT0128819 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020505 | SBNO1
Description
strawberry notch homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:HGNC:22973]
Coordinates
chr17:54523863-54524812:+
Coord C1 exon
chr17:54523863-54523998
Coord A exon
chr17:54523999-54524699
Coord C2 exon
chr17:54524700-54524812
Length
701 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAAT
5' ss Score
4.94
3' ss Seq
TTTTTTTAATGTCGTTACAGGAC
3' ss Score
9.08
Exon sequences
Seq C1 exon
AATATTGCTATCATCTCAGAAGCTGCCAGCTCAGGTATTTCATTACAAGCGGATAGAAGGGCTAAAAATCAAAGGCGAAGAGTTCATATGACTCTGGAGTTACCATGGAGTGCTGATAGAGCAATTCAGCAATTTG
Seq A exon
GTAAATCCTGCACTGAATTTCATTTCATTGGGGAAAATACTTTAATATTGGACATAGTAAAACTTGACGCGTGTGTCGGTTTTGGAGATACTTAGGTATTGCATGTACCTTAAAGAATAGAGTACATCATGAATGTATTTTCTTAGTCATAAAAGCTGTAAAAGACCTGAAGTAGGGCTTTCTGGCTTTATATTCAAGAATGGGGCTCCTTAGGAATATCCTTCTTGCAGACCTCTGGGGATGTATATTACCTGTGTCAGCAGCTGCCACTTGATGTCCTTTTCAACCCCCAGTGGCTTGAGTGAGGGCACATTGCTCCTCCCTTCCCCTCCATCTTCATGTCCCATGACCTGGCAATTAAAAAAAAAAAGGAAAAGAAAAATTTAAAAAAATTTTTCTTTGAGAATCCAGAGCAGCTGTGCATCAGCAACATTGTGGTCATCCAAACTGGGGTAGCACTTAAGCGATTATCACTTAACAGTTTTATGGGAGTTTTTGTTCTCTTGCAATGAGGAGTGTTACTCTGAATACAAATGTTGTTCAAGTCATTGTTTGCAATTTTTTCCTTTTTGGGGAATTGGGGTGATTACATTCTTTACTTTTTCAGGATACCAGCTTACTCTTAAGTGCTAGGAATAGATCTCATAACACTAGTACTGAGCAAACACAATCAGTGATTTTTTTTTTTAATGTCGTTACAG
Seq C2 exon
GACGAACTCATAGATCAAATCAAGTTACCGCTCCTGAATATGTCTTTCTGATTTCTGAATTGGCAGGAGAACAAAGATTTGCATCTATTGTTGCTAAAAGACTTGAGAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020505:ENSBTAT00000027325:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.217 A=NA C2=0.079
Domain overlap (PFAM):
C1:
PF138711=Helicase_C_4=FE(16.2=100)
A:
NA
C2:
PF138711=Helicase_C_4=FE(13.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGCTATCATCTCAGAAGCTGCC
R:
CAAACTCTCAAGTCTTTTAGCAACA
Band lengths:
246-947
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development