RnoINT0132818 @ rn6
Intron Retention
Gene
ENSRNOG00000016512 | Sema3b
Description
semaphorin 3B [Source:RGD Symbol;Acc:1310079]
Coordinates
chr8:116355048-116355331:-
Coord C1 exon
chr8:116355276-116355331
Coord A exon
chr8:116355188-116355275
Coord C2 exon
chr8:116355048-116355187
Length
88 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TTTTACATTTTTGTCTCAAGACC
3' ss Score
6.2
Exon sequences
Seq C1 exon
GCGGTTCCGGAGGCAAGACATAAGGAATGGCAACCCCAGCACCCTGTGCTCTGGGG
Seq A exon
GTGAGTACCCCATCAGCTCCTACCCCCAGGCCTTGAAATTGCTACATCTAGTCCTGCCTTGTCTGAATTTTTACATTTTTGTCTCAAG
Seq C2 exon
ACCCCTCTCACTCTGTGCTGCTGGAGAGGAAGGTCTTAGGTGTGGAGAGGGGCAGCGCGTTTCTGGAGTGTGAGCCCCGCTCGCTCCAGGCGCATGTGGAATGGACCTTCCATCGTGCAGGGGAGGCAGCTCACACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016512:ENSRNOT00000066296:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.300 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(31.1=100)
A:
NA
C2:
PF0143720=PSI=PD(9.8=12.8),PF0768612=V-set=PU(47.8=93.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGAGGCAAGACATAAGGAA
R:
CCTGCACGATGGAAGGTCC
Band lengths:
171-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]