RnoINT0162613 @ rn6
Intron Retention
Gene
ENSRNOG00000050430 | Vav1
Description
vav guanine nucleotide exchange factor 1 [Source:RGD Symbol;Acc:3951]
Coordinates
chr9:9638493-9638792:-
Coord C1 exon
chr9:9638724-9638792
Coord A exon
chr9:9638580-9638723
Coord C2 exon
chr9:9638493-9638579
Length
144 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
TCACCATTTCCTACTCACAGGAC
3' ss Score
9.6
Exon sequences
Seq C1 exon
GAGCTAGTGAAACACACACAGGATACTACAGAAAAGGAGAACCTGCGGTTGGCCCTGGACGCCATGAGG
Seq A exon
GTGAGGGAGCAGGTGCTGCTGGTTGGGTACCCATGCTGGCAGCGACCTCTCTGCTCAACTGGGGGCTGACCCTTCACCCTTGGCTGTGGAAGGGATTGGGCCAGGGGGTAGGCAAGAAAGCTTCTCACCATTTCCTACTCACAG
Seq C2 exon
GACCTGGCGCAGTGTGTGAATGAGGTCAAGAGGGACAATGAAACCTTACGGCAGATCACAAACTTTCAGCTGTCCATTGAGAACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000050430:ENSRNOT00000073294:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.043 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062115=RhoGEF=FE(12.6=100)
A:
NA
C2:
PF0062115=RhoGEF=PD(4.0=24.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAAGGAGAACCTGCGGTTGG
R:
CAGGTTCTCAATGGACAGCTGA
Band lengths:
125-269
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]