DreINT0131736 @ danRer10
Intron Retention
Gene
ENSDARG00000063097 | scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:ZFIN;Acc:ZDB-GENE-050302-78]
Coordinates
chr4:8917836-8920058:-
Coord C1 exon
chr4:8919939-8920058
Coord A exon
chr4:8917947-8919938
Coord C2 exon
chr4:8917836-8917946
Length
1992 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGT
5' ss Score
8.02
3' ss Seq
TGTGTGCTTGTGTAATTTAGACT
3' ss Score
6.93
Exon sequences
Seq C1 exon
AGGCGGTAAAATGCCTCCAGAATGGAAAACCGCCACCACGTGCTCAACTCAGCTGCACTAAGACAGGTGGAGGAGAGGTGTGTTCACTTTCCTGTCCATCAAACGCACTCTTTCTAGCAG
Seq A exon
GTTAGTACCTCATTTTTGAGGAAGGTAAGTGTTGCTTAGAAATTGCATGCCATGAATTGCAGTTTAAAGGCAAATATTTACACTTATTAGGTACACAGGTTAGGTTGTTAGGTTGAACAGAAGATTCAACAAGGTTCTGGAAATATTCCTCACAGACTTCGGTCCATGTTGACATGATAGCATCACGCAGTTGCTGCAGATTTGTAGGTTGCACATCCATGATGCAAATCTCCCGTTCCAGTACATCCCAAAGTGCTCTATTGGATTGAGATGTGGTGACTGTGGAGGCCATTTGAGTACTTTGAACTCATTGTCATGTTCAAGAAACCAGTCTAAGATGATTTGCGCTTTATGACATGGTGCGTTATCCTGCTGGAAGTAGCCATCAGAAGATGGGTACACTGTGGTCATAAAGTGATGGAGATGGTCAGCAACAATACTCTGGTAGGCTGTGGCGGTGACATGATGCTCAATAGTTACTAATGGGCACAAAGTGGGCCAAGAACAGATCTCCCACACCACCACCACCAGCCTGAACGTTAACGAGCAGTTGGACAGGTGTACCTAATAAAGTGGCCGTTGAGTGTATGTAGGTTTAGCCCTGCTTTCATGGTTGTGGGCAGAAACTGTTGCTGTCCTATGCTGCTCTCTAGTGGTTGATAACTTGCAACATTTTTTGCATGCTTCGCCCAAAATGATTCACTTCAATGTGATTTTTGACACTGATGTGGGAAAGGAATGTTGAAATGATATTTCATATCATCTCTGAGGAACTGATTTGTTAAAGGTATTAAGGTGTTACATGACCAAAACTTCTCTCTGACAATTTTTTTTGCAAGGATCATTGGCTTGGAGGAATGTGTATAAACATATTAGCACCCAGCAGTAACTTTTAAAAAATACCTGATATACAAATTCACACAGATCTTACAAAAGGGCCACATTTTCCCCAACTACAGTTAAATACTGTGCACAACAGTCTGTTCTCCACTTCCAAAAACAAAAAATACTTTTGGTTATTTAAAGCACAAAGGTTGTAAAATATACTATGTTTCATGGTTAAAGCAAGATAATCATGACTTATATAATACTGTAAGTGATGCGAATATATTTTCAGAATTTCAGATAATATAATTTTTTATAAATACAAATGTAAAAAATATATATTGTCCAAAAAGATATATGGTGAAACATATGGCGAAACATCCCAATGCAATATTAAAATTGATATGCACAAAAAAGTCTAGTAAGTACTGCGAAATATTCCACATTTCTGATCATTTATCTTAAAAATTGCAGAGAACATTTTTTTTAATCACTGATAAATAAACTAAATAAACTGTAAAACAATACTGAAGAAAGCAATTTACCAATGCAGAATTGACAGAAGCATTAATAACATGCACTATACATTCTAGCATGCACTCCAAAAATAGGTATGCACCAATCCGGAAAGAATATACCAGAAAAAATCAAGCGAATAAAAAACTTTCATCTGTAAATATGATGTTTGCAAATCTTAGTATATAATCGTTTGTTTTTATGTGCATCTTTGTGTGTGTGTGTGTGTTTATGGCTATGGATTCTCTGTGCTTGTGTGTTAATGGTCTCCCGGGTTCACGCAGTGAGCTCTAAAGCTGCATAAAACCTCTTTTAATCCTGTTCACCCGGGGTCTGGAGCCTCATGCCAACAGAAATACTCAGCCTGCCATTGGACGATTTGTGGCAAGGCCGAAGTCAGGCCAATGACTCTCTAGACAACTTCCCAGTACTCTATCTTCCTGACAGCCAGCCTTCTATTCACACACACACACACACACACACACACACACACACACACACACACAATCATGCACAAGCACAACAAAATATTACTCAGGTGCATGAACCACCTGGAACATCTGTTTAAATGTGTTTTTGTGTGTGTTTGTGTGTGTGTGTGTGTGTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGCTTGTGTAATTTAG
Seq C2 exon
ACTCAGAAAACAGTTATACACTGAGCTGCGGTGTACCTGTCCAGCCAGGTAAAGCTCCACTGAAGAGAAACATCACAACTTCCAGCAGCAGCTCCCTGCAAACCTGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000063097:ENSDART00000091876:12
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=0.132
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:
GCGGTAAAATGCCTCCAGAATG
R:
CAGGTTTGCAGGGAGCTG
Band lengths:
224-2216
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]