DreINT0131106 @ danRer10
Intron Retention
Gene
ENSDARG00000060865 | scai
Description
suppressor of cancer cell invasion [Source:ZFIN;Acc:ZDB-GENE-060526-57]
Coordinates
chr5:31442260-31442666:+
Coord C1 exon
chr5:31442260-31442332
Coord A exon
chr5:31442333-31442492
Coord C2 exon
chr5:31442493-31442666
Length
160 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTCC
5' ss Score
0.87
3' ss Seq
TTTTCTTGGCTCGCTCATAGACC
3' ss Score
7.4
Exon sequences
Seq C1 exon
AATTTCTCCAATCTGTTCGGCCAGCCCCTTGTTTGCCTGCTTTCTCCAACAGTATATCCGAAGAGCATGCAAG
Seq A exon
GTCTCCTTTTTTTGTTGTGCTAATGTGTTGAGACATCAAACATTGCGATATTTGCTAAGCTTTTTTTCTTTCTTTCTTTAAAGTAGTATTTTTCTATTATTATGCTGCTCCTCTATTGTATTTTTAACACTGTTGTTGTCTTTTCTTGGCTCGCTCATAG
Seq C2 exon
ACCAGTCTCAGCGTGGGAGTCTGTTTACTCTCTTCCTTTACAACCCCCTCATGGGCTTCCTATCTGTCTGTGGACTGAGCAGCATGCGTTATGGATTGTGGGAAAAAGCCCAGGAACTCCTGCGGAAGGTTTTCCATGACATTGGCCAGATGATCACAAGTTCACGAGTTATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060865:ENSDART00000139744:14
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:
PF120703=DUF3550=FE(4.8=100)
A:
NA
C2:
PF120703=DUF3550=FE(11.7=100)
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:
AATTTCTCCAATCTGTTCGGCCA
R:
ACTCGTGAACTTGTGATCATCTGG
Band lengths:
242-402
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]