RnoINT0131938 @ rn6
Intron Retention
Gene
ENSRNOG00000000500 | Scube3
Description
signal peptide, CUB domain and EGF like domain containing 3 [Source:RGD Symbol;Acc:1304880]
Coordinates
chr20:7740260-7740976:+
Coord C1 exon
chr20:7740260-7740475
Coord A exon
chr20:7740476-7740814
Coord C2 exon
chr20:7740815-7740976
Length
339 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGG
5' ss Score
8.37
3' ss Seq
CGCGGCCGACTCTCCCTCAGTCA
3' ss Score
5.74
Exon sequences
Seq C1 exon
CTGGCTGTGGGCTGACTTGCCTCCGACAGCGGATGGAACGAAGGCTGAAAGGGTCCCTGAAGATGCTCAGAAAGTCCATCAACCAGGACCGGTTCCTGCTGCGTCTGGCCGGCCTTGACTATGAGCTAGCCCACAAGCCAGGCCTGGCAGCTGGGGACCGAGCAGAGCTAGTGGAGGTCTGCCGACCCGGGCAGCACCGAGCAGGCACCAAGTGTG
Seq A exon
GTAAGGGAGCTGGCTGGGAGGCAAGGGGGTGGGAGTGGGGAAGCCCAGCTTGGCCCTGGCTCAGAGCAGAGCAGGACCCCTTGCCTCAGGTGAAGCTCTCAAAACATGAGGTAGCAAAGACCCTGTCCACGGGCCTCCTTTTCCCAGTCCTAGGCTGAAATCTAGGGTACCAGGCAGGGCCAGCAGTTCTCCTGCACACAGACTTGACGTCCCTATCTCTCCAAGCAGGATTCCGCTCGTTCCCTAATAGATCTCCCATGTCCAGAGGAGCGGGAAGGGGGGTCTTAGGCCTGGGTGGTGGGAGATGGGGGGTGGCTAGCGCGGCCGACTCTCCCTCAG
Seq C2 exon
TCAGCTGCCCGCAGGGAACGTATTACCACGGCCAGACGGAGCAGTGTGTGCCATGCCCAGCGGGCACCTTCCAGGAGAGGGAAGGGCAGCTCTCCTGCGACCTTTGCCCTGGGAGTGATGCCCACGGGCCTCTTGGAGCCACCAACGTCACCACGTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000500:ENSRNOT00000000593:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.041 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=87.3)
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:
GACAGCGGATGGAACGAAGG
R:
GTGGTGACGTTGGTGGCTC
Band lengths:
346-685
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]