DreINT0131784 @ danRer10
Intron Retention
Gene
ENSDARG00000011490 | scube3
Description
signal peptide, CUB domain, EGF-like 3 [Source:ZFIN;Acc:ZDB-GENE-060717-1]
Coordinates
chr23:41424709-41425028:-
Coord C1 exon
chr23:41424876-41425028
Coord A exon
chr23:41424789-41424875
Coord C2 exon
chr23:41424709-41424788
Length
87 bp
Sequences
Splice sites
5' ss Seq
ATGGTGCGT
5' ss Score
8.27
3' ss Seq
ATATGTTTTGTCCTCTTTAGAAG
3' ss Score
8.69
Exon sequences
Seq C1 exon
GGTCTGCAACCTCTATTACCACCTATGAGACGTGTCAGACATACGAGAGACCGATTGCATTTACAGCCCGATCGAGGCGCCTCTGGATCAACTTCAAATCCAATGATGTGAACAGCGCTCGTGGTTTCCAGATTCCATACGTCACTTATGATG
Seq A exon
GTGCGTCACGAGATCAGTCTTTACATGTGATCCTTGCTATTATTAGTGTTCGCTGTCTCTTAGATGCATATGTTTTGTCCTCTTTAG
Seq C2 exon
AAGACTATGAGCAGCTGGTTGAAGATATCGTAAGAGACGGACGGCTTTATGCCTCTGAAAACCATCAAGAAATACTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011490:ENSDART00000102879:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(41.8=88.5)
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:
TGTCAGACATACGAGAGACCGA
R:
GCATAAAGCCGTCCGTCTCTT
Band lengths:
173-260
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]