MmuINT1029529 @ mm10
Intron Retention
Gene
ENSMUSG00000022469 | Rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:MGI Symbol;Acc:MGI:2441741]
Coordinates
chr15:97750006-97750394:-
Coord C1 exon
chr15:97750260-97750394
Coord A exon
chr15:97750155-97750259
Coord C2 exon
chr15:97750006-97750154
Length
105 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGAG
5' ss Score
4.86
3' ss Seq
ATTATGTACTGGGCCCCCAGCAC
3' ss Score
3.2
Exon sequences
Seq C1 exon
ACCCCACACCCTGAGCAGCTGGGCCCCACTCTGGGTTCTTCTGAGATGCTGGACCTAGTGAGCGCCAAGGACCTGGCAGGCCAGCTGACCGACCATGACTGGAACCTCTTCAACAGGATCCACCAGGTGCAGGAG
Seq A exon
GTAGAGCAGGAGGAGGAGGGTGTGGGCGGGACACCAGGCCTAGCATGCTGACCTGGTCTTTGGCCCGTCCAGGTGGAGCTGATCCATTATGTACTGGGCCCCCAG
Seq C2 exon
CACCTGCGGGATGTCACCACCGCGAACCTGGAGCGCTTCATGCGCCGCTTCAACGAGCTGCAGTACTGGGTGGCCACAGAGCTCTGTCTCTGCCCTGTTCCTGGCTCCCGGGCTCAGCTACTCAGGAAGTTCATCAAGCTGGCAGCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022469:ENSMUST00000129223:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.195 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(15.2=60.0)
A:
NA
C2:
PF0061714=RasGEF=PU(26.3=97.3)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGTTCTTCTGAGATGCTGGA
R:
GGCTGCCAGCTTGATGAACTT
Band lengths:
251-356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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