RnoINT0131934 @ rn6
Intron Retention
Gene
ENSRNOG00000000500 | Scube3
Description
signal peptide, CUB domain and EGF like domain containing 3 [Source:RGD Symbol;Acc:1304880]
Coordinates
chr20:7738961-7739315:+
Coord C1 exon
chr20:7738961-7739077
Coord A exon
chr20:7739078-7739210
Coord C2 exon
chr20:7739211-7739315
Length
133 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAG
5' ss Score
8.73
3' ss Seq
TGATAGTCCCCTTCTCTCAGAGT
3' ss Score
6.06
Exon sequences
Seq C1 exon
AGCCAGTGAAGTGCCAGAGCAGTTCTGGAGCCTCAAAAGCCATGCTCAGCTGCAGTCGCTCGGGCAAGAAGGATACCTGTGCCCTGACCTGCCCCTCCCGCGCCCGGTTCTTACCAG
Seq A exon
GTATAGGGAGGGTGGGGCTTTGGGGAGAAGGGAGGGGAGACTGGCTGTTCGACAGTTCCTCTGTTCCCAGGGACAACTCCGACCACTGGGGGTTGAGGGGCGGGTCAGAGCTGTGATAGTCCCCTTCTCTCAG
Seq C2 exon
AGTCAGAGAACGGATTCACAGTGAGCTGCGGTACCCCGAGCCCTAAAGCTGCTGCAGGTCGAGCCATTCACCCGGGCAACAGCACCATCTCCAACTCCTGCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000500:ENSRNOT00000000593:11
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=0.111
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GCCAGTGAAGTGCCAGAGC
R:
ATGGCAGGAGTTGGAGATGGT
Band lengths:
220-353
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]