RnoINT0132884 @ rn6
Intron Retention
Gene
ENSRNOG00000017704 | Sema3f
Description
semaphorin 3F [Source:RGD Symbol;Acc:1308514]
Coordinates
chr8:116442841-116443208:-
Coord C1 exon
chr8:116443167-116443208
Coord A exon
chr8:116442999-116443166
Coord C2 exon
chr8:116442841-116442998
Length
168 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CTCCCTGCTCCCACTCCCAGCAA
3' ss Score
7.87
Exon sequences
Seq C1 exon
GAGCCAGCACCTGTTAAAACTATGACCATCTCTTCCAAGAGG
Seq A exon
GTGAGTCCTTGGCAGTGTGGGCTGGAGTGAGGTTGGAGCCTATGTCCCCTTGGGGTCATGCCCTTGGCATAAGGACTAGGAGACAGAAACAGAAAAGGAATCCAGCCCAGCTGGCTGCTGACAGGGCTGTCTGAGAAGGGAACTGACGCTCCCTGCTCCCACTCCCAG
Seq C2 exon
CAACAACTGTATGTGGCCTCCGCCGTGGGCGTCACACACCTGAGCCTGCACCGCTGTCAGGCCTATGGAGCTGCCTGTGCTGACTGCTGCCTCGCCCGAGATCCCTACTGTGCCTGGGATGGCCAGGCCTGCTCTCGCTACACAGCATCCTCCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017704:ENSRNOT00000024193:15
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=FE(2.7=100)
A:
NA
C2:
PF0143720=PSI=PU(66.0=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCCAGCACCTGTTAAAACT
R:
CTCTTGGAGGATGCTGTGTAG
Band lengths:
200-368
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]