GgaINT0006903 @ galGal4
Intron Retention
Gene
ENSGALG00000003392 | SBNO1
Description
protein strawberry notch homolog 1 [Source:RefSeq peptide;Acc:NP_001026640]
Coordinates
chr15:5007528-5008892:+
Coord C1 exon
chr15:5007528-5007624
Coord A exon
chr15:5007625-5008731
Coord C2 exon
chr15:5008732-5008892
Length
1107 bp
Sequences
Splice sites
5' ss Seq
AATGTATGA
5' ss Score
2.55
3' ss Seq
CCCGTTACCTTCCCAACCAGTAA
3' ss Score
6.24
Exon sequences
Seq C1 exon
AAAGTTCCAGCTGTTAAAGAGGAGGAGGAACCTGAGGAAGAAGACGAGGAAGAAATGGGCCATGCAGAAACTTATGCAGAGTATATGCCAATAAAAT
Seq A exon
GTATGACCTACATCTTGGCTGTATCAAAAAGCTGAACCATTGAAAGCTATAATGTAACAACTATGGCAGAGTAACTAGCATATGCTCAAATTCCCATAGGATTTTTACTGGATTGAATAAAAAAAAGACTATAATTTAGGGTGTTTTTTTCCTTTAGGTATTTTTTTTACATAGCACTCAGTTTTGAAAGTACACTATTGTTTTTTAATAGGAAGAGAATTCTTTCACAAGTGCCGTTAAACCAAAATGTTTTGATTTGTTTTTTAACCTGTGTTAAGCTTTCTTCTTCAGCAGAGAAAATTACCTTGTAAAAAGGATTAAGTGTTCACTGCTACACTTACAAATTCATTTTGAGTCTTTAGGAGTGAAGTTTACCCTAAGCATTTTCTGCCTATGTTGTTCCTTGCTTATTTTCCAGAACTGACTTTTTTCTTCAAAAAGGAGATATCTTTTACAGCTGTTAATTGCTGTTTCCTCCTTTTTTTTCCTATTTATTGTCATTAGTGATAAAAAGGTGTGATCTTACTTCCTAATTATTTTGAACTGCTGTAAAAGCAAAACAAAAGGAAAACGTTGCACGGTGTTTGTAGTTAAATGTTTTTAGTCACAAATTAGATCTGTCAGTACTTAAACTATGTCTGTTCTAAATTTTTTTTCTCCTTTCAAACTACTTATAAACAGCACTATATAAATAGAAGAATGTTGCTTTTGTGATTCTGGCATCTTGAGTCTGCCTCTCTTGGGTGGGAGAGACAAGGTTCAGGGCAGTTTCTCTCATATCAAATACATATCTGGTTTTGATTTTTTTTTTTATGAAATGAACTTTTATCTATTTTCATTTTTAAAAAGTAGGGTAAGATGGTGAGAGAAGAAACAAAGTTAAGAATGGCTGTTATTATATAAACTCGGATTTATGTATTGCTTTGCATGTGGAAGTTTAACTCTCAATTTTGAGTAAGCAATTAAATGTGTCTATCAAGTTAACCTTTGTTGTGAACAACTGCAGTTTATTTTAGTAAATATAATAACCTGTGCTGCAGCAACAAAGCTGTTTATTATGTTCTCATCTTTTCCTCTTTCCCTTCTTCCCGTTACCTTCCCAACCAG
Seq C2 exon
TAAAAATTGGTCTACGTCATCCTGACCCAGTAGTGGAAACCAGTTCGTTGTCCAGTGTAACACCTCCTGATGTGTGGTACCAGACATCGATATCAGAAGAGACCATTGATAATGGCTGGTTGTCAGCTTTGCAGCTTGAAGCAATCACTTATGCAGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003392:ENSGALT00000005363:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.712 A=NA C2=0.083
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCCAGCTGTTAAAGAGGAGGA
R:
TGGGCTGCATAAGTGATTGCT
Band lengths:
254-1361
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]