RnoINT0133710 @ rn6
Intron Retention
Gene
ENSRNOG00000025892 | Set
Description
SET nuclear proto-oncogene [Source:RGD Symbol;Acc:1307467]
Coordinates
chr3:8646030-8646503:+
Coord C1 exon
chr3:8646030-8646157
Coord A exon
chr3:8646158-8646319
Coord C2 exon
chr3:8646320-8646503
Length
162 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGG
5' ss Score
4.94
3' ss Seq
TATTTATGTCTCCTCTGTAGGCT
3' ss Score
9.49
Exon sequences
Seq C1 exon
GCCCTGACTTGCTGGCAGAGGAGTTGCAGCACCGACTGCGAATAGAGGCTGCTGTGGCTGCAGGTGCCAAGAATGTGGTGAAGCTGCTTGGTGGCCAGAGAATTCAGGACCGCAAGGCACTGGCCGAG
Seq A exon
GTCAGGCCCTGTCCTCTGCCTCATTGCTTTCTCTGCGGACTGCTTGTCTCCCTGGTGCCTGCACCAAGGGCTTCCTGCCTGTGTTGGGTAGCAGTGAAGACCCACGAGGAGGTGCGGCCTGAGCCCATTAACCCATCCCCGCTATTTATGTCTCCTCTGTAG
Seq C2 exon
GCTCAGGCCCAGCTCCAGGAATCCTCCCAGAAGCTGGACCTCCTACGGCTGGCCCTGGAATTGTTACTGGAGAGGTTGCCTCCCACCCACTCTCTTCGCAGCAGGGTGACCCGAGAACTGCGGATGGCCATGCTTGGGAACCCCCAGCCTCTGGGGACACTTGTGAAACCCATTGCCCTGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025892:ENSRNOT00000050528:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.193 A=NA C2=0.105
Domain overlap (PFAM):
C1:
PF0218511=HR1=PD(4.3=4.7),PF0218511=HR1=PU(54.2=90.7)
A:
NA
C2:
PF0218511=HR1=PD(43.1=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGTGCCAAGAATGTGGTGA
R:
GTCAGGGCAATGGGTTTCACA
Band lengths:
250-412
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]