MmuINT0172667 @ mm10
Intron Retention
Gene
ENSMUSG00000034116 | Vav1
Description
vav 1 oncogene [Source:MGI Symbol;Acc:MGI:98923]
Coordinates
chr17:57303015-57303943:+
Coord C1 exon
chr17:57303015-57303147
Coord A exon
chr17:57303148-57303833
Coord C2 exon
chr17:57303834-57303943
Length
686 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGA
5' ss Score
6.03
3' ss Seq
CGATGTTTTTCCACACACAGTGG
3' ss Score
5.42
Exon sequences
Seq C1 exon
GTATGCCTTCCTGCTGGACAAAGCACTGCTCATCTGTAAACGCCGCGGGGACTCTTACGACCTCAAAGCCTCGGTGAACTTGCACAGCTTCCAAGTTCGAGATGACTCCTCCGGGGAGCGAGACAACAAGAAG
Seq A exon
GTGGGACTCTGCCACCGGGTCTCGGGGGTTGCCTGCATGTGGAAGAGAGACACAGAGAGAGTGAGAGCAAGAGCGAGTTTAAGGACCTTGGGGTTGCCTGAATGTGGGGAGAGAGAGAGGGAGAGAGAGAGGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATTTAAAGACTTGTCCTTCAATCTTCTCAATCTCATTGAAAAATTCTTGTGTGAGTTAGAGTTCAGAGGCAACCTCAGGGACCATCCATCTTTTAAAATTTTTATTATTTTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTGGAGACAGAGGCTCTCACTGAGCCTGGGGCTTGCCATTTAGGCTAGGTTGGCTGACCAGGGAGGCCCAGAGTCTCCCGTGTGTCTGCTTCCCCAGCTCTGGAATTATAAGCACATGACATCACTCTTGATATTTTTAATGTAGGTTCTGGGGTTTGAACTCAGGTCCTCATTGACTGTTGGACTTGCTGATGTGTGTTTGGATGGTCTAGACAGCCTTGTTTGAACACACCCATGTATGTGCCCTGGGCAAGAGTAGCTTATTACTCTGAGGGATGAAGGACAGGTGGGATGTGATCCTGCCTACTGCAGGGGATCCATTTGCGATGTTTTTCCACACACAG
Seq C2 exon
TGGAGCCATATGTTCCTTCTGATTGAGGATCAAGGCGCCCAGGGCTATGAGCTGTTCTTCAAGACTCGGGAGCTGAAGAAGAAGTGGATGGAACAGTTCGAAATGGCCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034116:ENSMUST00000005889:14
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:
PF0016924=PH=FE(43.1=100)
A:
NA
C2:
PF0016924=PH=FE(35.3=100)
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:
ATGCCTTCCTGCTGGACAAAG
R:
TGGCCATTTCGAACTGTTCCA
Band lengths:
240-926
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