DreINT0131743 @ danRer10
Intron Retention
Gene
ENSDARG00000063097 | scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:ZFIN;Acc:ZDB-GENE-050302-78]
Coordinates
chr4:8908864-8909383:-
Coord C1 exon
chr4:8909222-8909383
Coord A exon
chr4:8909062-8909221
Coord C2 exon
chr4:8908864-8909061
Length
160 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGA
5' ss Score
6.91
3' ss Seq
ATGCCGCTGGTCTATTCCAGATC
3' ss Score
8.64
Exon sequences
Seq C1 exon
TTCACTGTGCTCTTGGCCATTATTATAATGCCACCACACATCGGTGCATCCGCTGTCCAGCTGGTACCTATCAGTCTGAATCCGGACAGAACTACTGCATCACCTGCCCTGGAAACACCACTACAGATTTCGACGGCGCTAACAACGTGTCTCACTGCAAAA
Seq A exon
GTAAGAGAAATACCCGCAAATCCATTCGTTTGTTTGTACGTATTGGTTTTTGCTGCACTGCAAATTAATGTGGCATTTAAGTTTTGAACTCATCCACAACCAATGAAACAAATGAAATGAAACAGTTTCGAATGGACTTCATGCCGCTGGTCTATTCCAG
Seq C2 exon
ATCAGATATGTGGTGGAGAGCTGGGCGACTTCATGGGCTACATCGAATCTCCGAACTATCCCGGTGACTATCCATCTAATGTGGACTGCGTCTGGACCATTAACCCTCCAAACAAAAGGCGGATCCTTATTGTTGTACCAGAGATCTTCCTCCCCATCGAGGATGAGTGCGGGGATGTTCTCGTCATGAGGAAGAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000063097:ENSDART00000091876:19
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:
PF076998=GCC2_GCC3=WD(100=87.3)
A:
NA
C2:
PF0043115=CUB=PU(56.4=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCTGGAAACACCACTACAG
R:
CTCATGACGAGAACATCCCCG
Band lengths:
247-407
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]