RnoINT0132886 @ rn6
Intron Retention
Gene
ENSRNOG00000017704 | Sema3f
Description
semaphorin 3F [Source:RGD Symbol;Acc:1308514]
Coordinates
chr8:116442199-116442687:-
Coord C1 exon
chr8:116442620-116442687
Coord A exon
chr8:116442333-116442619
Coord C2 exon
chr8:116442199-116442332
Length
287 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
AGGGTCCTCTTGATCCACAGCAA
3' ss Score
5.9
Exon sequences
Seq C1 exon
GCGGAGTCGCCGACAAGATGTCCGCCACGGGAACCCCATCAGGCAGTGCCGTGGTTTCAATTCCAATG
Seq A exon
GTAAGTTAGCACGTTGCTCCTCCTGTAGGCTGCTTCTCATGGTGTGGAGTCCTATGCAGCCAATGCGCACAGGCACCCTCACAGTCCAGACTTACTTATGGTTCCCTAGGTGGCAGGATCACCTTAGGCCTGGGATTAAAAAGTCCCATGTCACCTCCTCAATGAATAGATACCCATCGATGTTGCCCTGGTTTTGCGCGTGGATGCCCCTTGATGCCTGCCTCCCCCTACTGGACAGACTGCCTTGCAGCAATGCTGCTTCCACTCAGGGTCCTCTTGATCCACAG
Seq C2 exon
CAAACAAGAATGCCATAGAGTCTGTGCAGTACGGCGTGGCCGGAAGTGCGGCTTTCCTTGAGTGCCAGCCTCGGTCACCTCAAGCCACTGTTAAGTGGCTTTTCCAGCGAGATCCCAGTGATCGGCGTCGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017704:ENSRNOT00000024193:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.292 A=NA C2=0.089
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(32.1=70.8)
A:
NA
C2:
PF0767911=I-set=PU(45.5=88.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGTCGCCGACAAGATGTCC
R:
CTCACGACGCCGATCACTG
Band lengths:
199-486
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]