DreINT0131738 @ danRer10
Intron Retention
Gene
ENSDARG00000063097 | scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:ZFIN;Acc:ZDB-GENE-050302-78]
Coordinates
chr4:8913768-8915429:-
Coord C1 exon
chr4:8915313-8915429
Coord A exon
chr4:8913927-8915312
Coord C2 exon
chr4:8913768-8913926
Length
1386 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGA
5' ss Score
6.65
3' ss Seq
GTTTCTTTTTCTTTCATCAGCTG
3' ss Score
7.93
Exon sequences
Seq C1 exon
AGATGCTGGCGCAGCCTGTGAAGCAGAAAGCCCGCTTTAAGATCAAAGACGCCAAGTGCCACATGAGACCCCGCAACAAGGAGAAACACAGAGACATGGGGAAGCAGGGCCTTCAGG
Seq A exon
GTGAGACATCATCACATCGCAAACGCTTCCAAATTAATTAAAAGATGAACAAAACAGATTGTGCTTCTTGTTCAAACTACTTATTTAAGATGAGTTGAAACTACACAATCCTCAAGTTTTTGGGGGGACAACTTAATTGTTTTATGTTTAATCCACATATATTTGTAAAAAAAAAAAAAAAAAAAAGCGATTAGGTTAACTTAATTGATTGGTTTTGAGACATGGAGAATTGTGTCACCCTGCATTTTTTACAGCGTGAATCCTCTCACGAAGTTCCACTTTTTCTGTTTGCCTTTGTTTAGCATTTTGTTCTCTCCTCCTTTATTTTTATTTTTTTGTTTCCATTTGTTGACCTTCTTCCATTTTCTGTTTTTTATATTTGTGTCCTTTTCATTTTCTCTTCCTGTTCATTTAATTTGTTTTGCTTCTTATGCCTTTTCATTTCCTGAATTATTTTCTTATTTCCACTTCTGACTTGTTTTGTTTCACGTCCTTCACTGCCGTTTTTTTCTGTTCTCTTTTCCCCATTATTTTTGTTTATTTTTAATCTTTCATTTTTCTTTTGCATGTTGTTTTCTCATTTCTTTCTCTTTTCTTTTCTCTTTCGTCTTACTTCCTTTACTTTTCCTGTTTCAGCTGCTGTTCATTTTTTCTTTCCTCTTCTTTCCTTTATTTTTGCATTTGTACTTTTATTTCCTTTTTATTTCCTTTGGAGCCAGCACCTAAGCTTTTCACTTATCATAGCACACGTGCTGCTGATGAGGTGACAAATAAAAGTGATTTGATTTGATTTCCTGTGTCATTTCATTCCTTTCATATTTTTCCTTTTTCATTTGTTTCCTGTTTTTCTTCCTATTGAGCATCTTCTGTTTCCTGTTTTTTATATATTTATATCCTTTTTATTTTCCGTTTCTTCTTCTTTTCATTTGTTTTGTTCCCTTTGTTCCCTTTTTATTTCCTGATTTATTTCCTTTGTTTTTTTTCCTCTCATTTATTTTGTTTCACTTTCCTCACAGCAATTTTTCCCATTCCTTTAATTGTATTGATTTCTATCTTCTTTTTCTGTTCTCTTTTCGTTGTTTTTTTTCATACTTTTGTTTTTTCTTTTCCATGTTGTTGTTTTCATTTCTTTTTCTTCTCTGTTCTCATAAGTCTTGTTTCTTTTCCTGTTTCAGCTACTGTTCATTTTCTTCTCCTGTTTCTCATTTCTCTTGTCTTTTTTCATTCTTCCTTTTTCTTTTTTTTTTTCCTCTTTTTCTTTATCTTTTGCCTTTGTTCCTTTATTTCCTTTTCTGTGCCAATTCCTTTCTCATCAGTTCTTCCTTATTCCTCTTTTGCTTTCCCTGATTCACTTTTCATATTTCATGTTTCTTTTTCTTTCATCAG
Seq C2 exon
CTGGCCAGTTCCCTTGCACAGACGACTGTCAGGTAACATTTGTGAATCTGAAGTGCGACTCTTCCAAAAAGCGCCGTAGGGGCCGGAAATCTCCCTCAAAGGAAGTCTCGCACATTACAGCAGAGTTTGAGATGGAAATGAAAGAAGAAGAAGCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000063097:ENSDART00000091876:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.575 A=NA C2=0.426
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAGCAGAAAGCCCGCTTTA
R:
TGAGGCTTCTTCTTCTTTCATTTCCA
Band lengths:
257-1643
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]