RnoINT0132889 @ rn6
Intron Retention
Gene
ENSRNOG00000017704 | Sema3f
Description
semaphorin 3F [Source:RGD Symbol;Acc:1308514]
Coordinates
chr8:116451219-116451546:-
Coord C1 exon
chr8:116451386-116451546
Coord A exon
chr8:116451282-116451385
Coord C2 exon
chr8:116451219-116451281
Length
104 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGG
5' ss Score
4.89
3' ss Seq
CTAACCTCCATCTTTGGCAGATC
3' ss Score
8.59
Exon sequences
Seq C1 exon
AACTTAAGGCCACAGGTACTGCCCACTTCTTCAACTTTCTGCTCAACACTACAGACTACAGAATCCTGTTCAAGGACGAGGACCATGACCGCATGTATGTGGGCAGCAAGGACTACGTGCTGTCCCTGGACCTGCATGACATCAACCGAGAGCCCCTTATT
Seq A exon
GTAAGGGCTGGCCTGGAAGTGGGACGAGGCAGGGTGAAGGGCGTGGAGCCCAGGGTCAGGGACCTGGCCAGCAGGCTGCCTTCTCTAACCTCCATCTTTGGCAG
Seq C2 exon
ATCCACTGGGCAGCCTCCCCACAGCGCATTGAGGAGTGCATATTGTCAGGCAAGGATGGCAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017704:ENSRNOT00000024193:3
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(28.1=63.0)
A:
NA
C2:
PF0140314=Sema=FE(16.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTACTGCCCACTTCTTCAACT
R:
GTTGCCATCCTTGCCTGACAA
Band lengths:
210-314
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]