DreINT0131778 @ danRer10
Intron Retention
Gene
ENSDARG00000011490 | scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:ZFIN;Acc:ZDB-GENE-060717-1]
Coordinates
chr23:41441085-41441956:-
Coord C1 exon
chr23:41441795-41441956
Coord A exon
chr23:41441289-41441794
Coord C2 exon
chr23:41441085-41441288
Length
506 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CATCTATTTTTCATGTTCAGGGA
3' ss Score
9.42
Exon sequences
Seq C1 exon
GCGGTCAGCCGTGCAACAACTGCCTGGTCACGTTTGTTAACCTGAAGTGTGACTCCTCTAAGAAGACCAAAGGCGGTCGTCGAGCTCGAAACCCGACAAATAAAGAGGTGACGCGCATTACTCTGGAGCTGGAGGCCGAGGTCAAACCGGGAGACGCAACCG
Seq A exon
GTGAGTAAAATAAAATAAAAAGGTTCATGTTATGTTTTTAATTTCATAAGGTTCCTTTTACAGCATTTATGTTGTAATGTAATTAAATTACAATCAGTTAAATTGACTTAAGCATTCATTTAGTTGTTCAAGTGTAAAACAAGATTAAAAACCGTTTAAACATAAGCGCCGTCAGGAGCAGAAGATGAGCGCTGAAACTCCATTGAAAGTACTGGGTTGACATGGCGCAGAACAATCGAATTTAATGCAGTGCTTCATGTCCAGTCTGAAACACTTTTTATACGATATCTTAATCGGCCAGTGAAGATCGCTGATTTTTAAACGCTGTGATTATTTTTTTCATGGCAAATTCACTGGAAGCGCTTGGACTGGCTGACTGAAAATCAAAAAGTCCCTGTGCATATGCCCCATTGGTACTTTAAGTGTAGTGTTAGCAAAAATGCAGTCTATTAATTAGGAAACGCGCTGTGTGAAAGTTCTGGCGTTCATCTATTTTTCATGTTCAG
Seq C2 exon
GGAACTGCAACATGATGTGTCAACGGCAGCACATGGAGCAGCAGATGAAGACGTACATTAAAACCCTGAAGAAGTCCATTAACCAGGAGCGTTTCCTGCTGCGTGTCGCTGGACTGGAGTATGAGGTGGCACAGAAGCTCACACAGACAGCGTTGAAGCAGGAGAACTGCGGACCGGGCCGAGAAAAGGACAGCGGACGTTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011490:ENSDART00000102879:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.436 A=NA C2=0.145
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACTGCCTGGTCACGTTTGTT
R:
AACGTCCGCTGTCCTTTTCTC
Band lengths:
346-852
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]