GgaINT0006912 @ galGal4
Intron Retention
Gene
ENSGALG00000003392 | SBNO1
Description
protein strawberry notch homolog 1 [Source:RefSeq peptide;Acc:NP_001026640]
Coordinates
chr15:5015440-5016223:+
Coord C1 exon
chr15:5015440-5015537
Coord A exon
chr15:5015538-5016071
Coord C2 exon
chr15:5016072-5016223
Length
534 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGA
5' ss Score
6.91
3' ss Seq
ATTTTTTTTTCCTTAAACAGAGG
3' ss Score
8.48
Exon sequences
Seq C1 exon
TGTGTTGTTATTGGCCTGCAGTCAACAGGAGAAGCAAGGACATTAGAAGCTTTGGAGGAAGGTGGTGGTGAATTGAATGACTTCGTTTCTACAGCAAA
Seq A exon
GTAAGATTGGGTCAGAATTGTGGTTTAAAAAACTAACCAGAATATAACATAATGTGTGTAGTAAAAGCTGTGTGTATGCAAGATCTTGACAGTATTGCTGTAGTGAGCTGTTCGTTAGTTCCTAGTTCTGCCAACACCATGCTAAATGGTGTTTCATGTGGAACTGCTGGTGCTGTTCTACTCCAAGTGGAAGGGAGAGTAGACTTGTGAAGTACATGCTATGGTTACACAGTCTTTTATCAGATGAGCAGATTTAAGTTTAAGTGTCAGATTAAATTATTTAAGCAGCAAGAAAATGTCAGTGGAAATAACACTATATACCAAAATCAAATTTAACAGGTTAAAGTATCATATCACTACTTTTTTAGAGGGTGACAGTGTGATATGGGTGATAATTATACAGGGTGCTTCTGTAATAGCATTCACAAGCAATAAATTGTTCATAGAAGTCATGCAAGCTACTGAAATGTTACTTAGAGGTTGTTACTTCAAATGAACACAGATCTGACTGAAGATTTTTTTTTCCTTAAACAG
Seq C2 exon
AGGAGTATTCCAGTCTCTTATTGAAAAGCACTTTCCAGCTCCTGACAGGAAGAAGCTGTTTAGCTTGTTGGGAATTGACTTGACTGCTCAAAGCAACAACAATTCACCCAGAGACAGCCCTTGCAAGGAGAACAAAATAAAGAAACGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003392:ENSGALT00000005363:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.030 A=NA C2=0.423
Domain overlap (PFAM):
C1:
PF048897=Cwf_Cwc_15=PU(0.1=0.0)
A:
NA
C2:
PF048897=Cwf_Cwc_15=PU(34.7=98.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGTTGTTATTGGCCTGCAGT
R:
CCGTTTCTTTATTTTGTTCTCCTTGC
Band lengths:
246-780
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]