GgaINT0141261 @ galGal3
Intron Retention
Gene
ENSGALG00000002675 | SCUBE3
Description
NA
Coordinates
chr26:3988398-3988834:-
Coord C1 exon
chr26:3988714-3988834
Coord A exon
chr26:3988521-3988713
Coord C2 exon
chr26:3988398-3988520
Length
193 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
CACTTCCTTTCCCCTTGCAGATG
3' ss Score
13.24
Exon sequences
Seq C1 exon
TTGGAGAAAGAGGCTTTCACCTCTAGCTGGGCTGGTTCCAGCCTGGACTTCTGGTGTCTGAGCATTGCTTCCCATCAGCTGTGTGAAATGATCACTGGCTCCCAAGGGAGCTTTAATGAGA
Seq A exon
GTGAGTGCACAGGTGATGCTGTTCTGGAGCACACCCATCACCAATTGCTCTGGGGCTGGGTGCAGTGATAGGGAGCAAAGCAGGGGAATTTCTCCCTTTTTCCTCCCCACTCTGTGTTGTGTTGCTTGAAAACTTGCATGGCTGCTACGGGTCTGTGTACTCCTTGCTCCCATCACTTCCTTTCCCCTTGCAG
Seq C2 exon
ATGTGGATGAGTGCGTGGAAGGCACTGACAGCTGTCACATTGATGCCATCTGCCAGAACACACCCAAGTCCTACAAGTGCATCTGCAAGTCCGGCTACACTGGTGATGGAAAGCACTGTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002675:ENSGALT00000004215:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF129472=EGF_3=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:
AGGCTTTCACCTCTAGCTGGG
R:
CTTTACAGTGCTTTCCATCACCA
Band lengths:
234-427
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]