MmuINT0172664 @ mm10
Intron Retention
Gene
ENSMUSG00000034116 | Vav1
Description
vav 1 oncogene [Source:MGI Symbol;Acc:MGI:98923]
Coordinates
chr17:57301861-57302160:+
Coord C1 exon
chr17:57301861-57301929
Coord A exon
chr17:57301930-57302073
Coord C2 exon
chr17:57302074-57302160
Length
144 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
TACTATTTCCCCACTCACAGGAC
3' ss Score
8.46
Exon sequences
Seq C1 exon
GAGCTAGTGAAACACACACAGGATGCTACAGAGAAGGAGAACCTGCGGTTGGCCCTGGACGCCATGAGG
Seq A exon
GTGAGTGAGCAGGTGCTGCTGGTTACCCATGCTGGCAGCAACCTCTCTGCCTCTACTAGCCGGCTGATTTTTTACCCTTGGTTGTGGAAGGGATTGGCCCAGGGGGGTAGGCAAGAAAGCTTGTTACTATTTCCCCACTCACAG
Seq C2 exon
GACCTGGCACAGTGCGTGAACGAGGTCAAGAGGGACAATGAAACCCTACGGCAGATCACAAACTTTCAGCTGTCCATTGAGAACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034116:ENSMUST00000005889:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 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
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACACACACAGGATGCTACAGA
R:
CAGGTTCTCAATGGACAGCTGA
Band lengths:
146-290
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types