GgaINT0141269 @ galGal3
Intron Retention
Gene
ENSGALG00000002675 | SCUBE3
Description
NA
Coordinates
chr26:3973441-3974259:-
Coord C1 exon
chr26:3974143-3974259
Coord A exon
chr26:3973564-3974142
Coord C2 exon
chr26:3973441-3973563
Length
579 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGG
5' ss Score
7.81
3' ss Seq
CTCTCCCTCTGTTCCCATAGATG
3' ss Score
11.9
Exon sequences
Seq C1 exon
ATATCGACGAGTGCTCCTTTGACCGGACCTGCGACCACCTCTGCATCAACACCCCTGGCAGTTTCCAGTGCCTCTGCAACAAGGGCTACACGCTCTATGGGCTCACCCACTGTGGAG
Seq A exon
GTAGGGCTGACTTGGGGGCTGAGCACTCAGGGCACCCAGAAATGGGGCAGCCCCATGGCTGTCCCCCAGGGCGGGTGGCAGTGTCCCACGTCCCCGCCGTGCACCCCATGCTGGGGCCGTGCAGGGAGAGCACATGTAGCCAGACGTTGGTGTCTGCAACTTCAAACGCAGCGGCAGGAACAATTTGCGACTTGTCTGCAGGGAGAGAGGGAGAGAAATCCCCAGCATTGTTGGCAGCGAGATGGGATGTGGGGTGGGAAGGGGAACATCAAAAGGGGTTGATTTAAGTTTGACGAGGCGGGGGCGTGCAGTGCCCCGGGATGCAGATGAAACATGCAGGGGGGGGGGGGGGGGGTGCAGGAGTGTGTTGTGGCAGCAGGGGGGTGACCTTACTCGTGCCACATGTGCCCCACTGCTCCTGGAGCAGCCTGCTCCAACCCAGCCCCCCCAGGATGCAAGAACCCCGCTGGTGTGTGTGCTTTGTGTCATTTATCTGTCCAAAATCACATCCCTGAGATGGTTCAGCATCAGAGCCGGGGGGTCCCGCTGCCCCCCCCACCTCTCCCTCTGTTCCCATAG
Seq C2 exon
ATGTTGATGAATGCAGCATTAACCGCGGAGGCTGCAAATTTGGCTGCATCAACACACCTGGCAGCTACCAGTGTACCTGTCCTGCCGGCTGCAAGCTGCACTGGAACAAAAAGGACTGCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002675:ENSGALT00000004215:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=95.0)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCGACGAGTGCTCCTTTGAC
R:
CTATGCAGTCCTTTTTGTTCCAGTG
Band lengths:
238-817
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]