DreINT0131734 @ danRer10
Intron Retention
Gene
ENSDARG00000063097 | scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:ZFIN;Acc:ZDB-GENE-050302-78]
Coordinates
chr4:8920144-8920972:-
Coord C1 exon
chr4:8920856-8920972
Coord A exon
chr4:8920267-8920855
Coord C2 exon
chr4:8920144-8920266
Length
589 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
CTGACATCTGTGCGTGACAGATA
3' ss Score
7.52
Exon sequences
Seq C1 exon
ATATTGACGAGTGCTCCTTTGAGAGGACGTGTGATCACGTCTGCATCAACTACCCTGGTAGCTTTGAGTGTGTTTGCCACAAAGGCTACAGTCTCTATGGCTTCACACACTGCGGCG
Seq A exon
GTGAGTTTTCAATGATTCCCACTAGGCATGGGACGATGACCGGTTTCAAGGTTTACCACGATTTGGAAAAGTCATGGTTTTAAAACTGCTAAAATTTTCCTATGGTGTATATAATATGTTTTTACATGGGTTTTTTTTTTACAATTATTTTGTCTAGTTTTTTAGGGCAACAGTATCTCCAGCAGCAAAAGACCATCCACATCAAAATCTACTGGTCAGCCCATGATTCTGGAAACATCTGTAAAACAAATCACCAATACACCAACATCTAAGCATAAAATAGACCTGAACACAGTGCAATGGCTTACTTTATATGCAAAGAAAAGAGAAATATCCAAAGATGGACTTTATATTGAAAAATATTAAAATATTACTATATTAAATGGGGGGGGGGGGGGGGGGGGAGTAGTTGTTTTTTACTCAGATAATTAAATAGAACATTTTAGAGCAGGAATCACAATATCGTGATATTTTCATCCAAGGTTATCATGCTGCCAGAATCATATACCGACCCATGCCTAGTTCGCACACTTTCAAAAAATATGAACAGCCACATTTTGATGAATTAACTGACATCTGTGCGTGACAG
Seq C2 exon
ATATTGACGAGTGCAGCATCAATAACGGAAGCTGTGAACACGGCTGTGTGAACACACCGGGCAGTTACGAGTGTGTGTGTCCTCCTGGACAAAAGCTCCACTGGAACAAGAAAGACTGTGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000063097:ENSDART00000091876:10
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=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=95.0)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGACGAGTGCTCCTTTGAGA
R:
CAACACAGTCTTTCTTGTTCCAGTG
Band lengths:
238-827
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]