DreINT0131740 @ danRer10
Intron Retention
Gene
ENSDARG00000063097 | scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:ZFIN;Acc:ZDB-GENE-050302-78]
Coordinates
chr4:8911643-8912112:-
Coord C1 exon
chr4:8911906-8912112
Coord A exon
chr4:8911805-8911905
Coord C2 exon
chr4:8911643-8911804
Length
101 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGC
5' ss Score
8.99
3' ss Seq
AATTTCTGTTTGTCTCCCAGTCA
3' ss Score
8.02
Exon sequences
Seq C1 exon
AATCATGCAACTTGGACTGCGTTCGCGAGAAAACCAAACAGCGATTACAGAACGCCATGCGCACACTAAGAAAGTCCATCAGTAAGCAACAGTTCTACATCCAGTTTTCTGGCACCGCATATGAAGTTGCCCAGCATGCTTTACGACATACGACTGAAGGAGATGAAACCTGCAGTATAGGACAGGTCTTTACCGATGGGAAGTGCG
Seq A exon
GTAAGCATTCTGGGAAACAAGGTTTTATCATGCTTTTATTTTCTTTCTGAAAGCACTTTTGTAAATCATGTTTTTTGGGTGAATTTCTGTTTGTCTCCCAG
Seq C2 exon
TCAGCTGCGTTGTGGGAACATTTTACAGTGGAGAACAGGAACAGTGCGTCATGTGTCCTCTTGGAACCTATCAAGACAGGGAAGGCCAGCTGTCCTGCGAGCCCTGTCCCAGAACTGAAGGACAGGGCATCGCAGGAGCCAAAAACGTCTCTGAGTGCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000063097:ENSDART00000091876:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=87.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCGCATATGAAGTTGCCCAG
R:
AGAGACGTTTTTGGCTCCTGC
Band lengths:
246-347
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]