RnoINT0131016 @ rn6
Intron Retention
Gene
ENSRNOG00000013987 | Sbno2
Description
strawberry notch homolog 2 [Source:RGD Symbol;Acc:1307194]
Coordinates
chr7:12504870-12505294:+
Coord C1 exon
chr7:12504870-12504966
Coord A exon
chr7:12504967-12505139
Coord C2 exon
chr7:12505140-12505294
Length
173 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
GCCCTCTGTCCCATCACCAGCCA
3' ss Score
6.14
Exon sequences
Seq C1 exon
TCACACAGCCAGCCTGAGGAGGAGGAAGGCGAAGACGAGGAGGAGGCTGAGGAACTGGGCCATGCTGAGACCTATGCCGACTATGTACCTTCCAAGT
Seq A exon
GTGAGTGTCCCAGCCAGGGACGGCATGGAGACACCCACTAAGATGAGGTCGAGTTCCCGATCCGTAGTGTGAAGGCACCAGGAGCAGGTTCTGTGAACAGGGTGGAAGACTGGCATGCTGCTGGCCTCTCTTCCTCTGTCATGTGCCAACTCTGCCCTCTGTCCCATCACCAG
Seq C2 exon
CCAAGATTGGAAAGCAGCACCCAGACCGTGTAGTGGAGACCAGCACACTGTCCAGCGTTCCGCCCCCAGACATCACCTACACCCTGGCACTACCCACCTCAGACAACGGGACCCTGTCTGCCCTACAGCTGGAAGCCATCACCTATGCCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013987:ENSRNOT00000068197:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.848 A=NA C2=0.462
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138721=AAA_34=PU(16.3=92.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCCTGAGGAGGAGGAAGG
R:
CTGGCAGGCATAGGTGATGG
Band lengths:
243-416
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]