GgaINT0006918 @ galGal4
Intron Retention
Gene
ENSGALG00000003392 | SBNO1
Description
protein strawberry notch homolog 1 [Source:RefSeq peptide;Acc:NP_001026640]
Coordinates
chr15:5020005-5020651:+
Coord C1 exon
chr15:5020005-5020140
Coord A exon
chr15:5020141-5020538
Coord C2 exon
chr15:5020539-5020651
Length
398 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAAT
5' ss Score
4.94
3' ss Seq
TCTTGTATTTAACTATCCAGGAA
3' ss Score
7.1
Exon sequences
Seq C1 exon
AACATTGCCATAATCTCGGAGGCTGCCAGCTCTGGTATCTCACTGCAAGCAGACCGTAGAGCTAAGAACCAGAGGCGGAGAGTTCACATGACTCTGGAGTTGCCATGGAGTGCAGACAGAGCAATACAGCAGTTTG
Seq A exon
GTAAATAACTTCTTTGTATCTTTTCCTCTTAGCCAATTCAGTAATGCTGAGTAAACTTGTTGCTCGTTCCTGTGAAGTTTGAAGCAGCCTTTTAAGGATCCTTCCAGTCTCCTTTACCTGTGGCAGAATTACTTTTATGTACAGTCATAGCTAATAGTCTCAGAAGCTTTGATAGAACCCTAGTGAACAAGTTTATACAGCGACTCAGCTTTGTATGTATCAAGTCTCTTCATGAAGTTACCCCAGCTCTAGTTTTGTGTACTGTTGGCTGGATTACAGCAAAAACTACTTTTCAGCAGGATTAAGTTATGGCTATTTTCTTTATGCAATTCATAGTTTATTAGAAATGGTAATTGAAGAATTTATTTTAACATATGTTCTTGTATTTAACTATCCAG
Seq C2 exon
GAAGAACTCACAGATCCAACCAAGTGACTGCTCCGGAGTACGTGTTCCTAATTTCTGAGTTGGCTGGAGAGCAGAGATTTGCATCTATCGTTGCAAAAAGACTGGAAAGCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003392:ENSGALT00000005363:20
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
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATTGCCATAATCTCGGAGGC
R:
AGCTTTCCAGTCTTTTTGCAACG
Band lengths:
246-644
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]