MmuINT0131708 @ mm10
Intron Retention
Gene
ENSMUSG00000022469 | Rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:MGI Symbol;Acc:MGI:2441741]
Coordinates
chr15:97757683-97758105:-
Coord C1 exon
chr15:97758017-97758105
Coord A exon
chr15:97757762-97758016
Coord C2 exon
chr15:97757683-97757761
Length
255 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCA
5' ss Score
6.37
3' ss Seq
ACCCTAACCCTGCCCAACAGAGA
3' ss Score
5.62
Exon sequences
Seq C1 exon
GTATACGGTCATGTCTGGCACCCCAGAGAAAATCCTAGAACTGCTGTTGGAGGCTATGAGACCGGATTCCAGTGCTCATGACCCAACAG
Seq A exon
GTAGCAACAGAAGACACTCTCCCTGTTCTCTGAGTCATCGGGAGGGTACTGCAGCCTGACCTCGGCAGGCTCTAGATTGGTGCATCCTGGCACTTGGCAGGAAGTGATCTTTGCTTGGGTGGAGAGAACTGTCACAGGGGCTGGGTGCTGCTCTCCTTGTTTGTGCTGACTTAGGGGACGTATATTCCGGGTGCCCATATAGGTGAGCTATGACTCGGGCTGAAATCCCTTCCCAACCCTAACCCTGCCCAACAG
Seq C2 exon
AGACGTTCCTCAGTGACTTCCTGCTGACCCACAGTGTCTTCATGCCCAGCACCCAGCTCTTCACTGCCCTCCTGCACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022469:ENSMUST00000129223:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.318 A=NA C2=0.012
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=PU(24.8=90.3)
A:
NA
C2:
PF0061815=RasGEF_N=FE(23.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTATACGGTCATGTCTGGCACC
R:
TGCAGGAGGGCAGTGAAGAG
Band lengths:
165-420
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