MmuINT0131729 @ mm10
Intron Retention
Gene
ENSMUSG00000022469 | Rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:MGI Symbol;Acc:MGI:2441741]
Coordinates
chr15:97758842-97759238:-
Coord C1 exon
chr15:97759162-97759238
Coord A exon
chr15:97758989-97759161
Coord C2 exon
chr15:97758842-97758988
Length
173 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TGATTGAGTTCTGGCTTCAGGGG
3' ss Score
4.03
Exon sequences
Seq C1 exon
TGTTCAGCCAGGGGGACAAGGGTACCTCGTGGTACATTATCTGGAAGGGATCTGTCAATGTGGTGACCCATGGCAAG
Seq A exon
GTAAGCCATCCCTCCAGCCCACTGGGATAGATGTCAACTGTCTTTGCTTCATGTCCTCATGGACACTCCCTTTGATAGCCCCAAGGCTGCTGATCCCACACATGTGGCCGAGTCTGTCCCTCCTACCAAGGGCTGGTGGGTAGGGACAGGCTGTGATTGAGTTCTGGCTTCAG
Seq C2 exon
GGGCTGGTGACCACGTTGCACGAGGGAGATGACTTTGGACAGCTGGCTCTGGTGAACGACGCACCTCGGGCAGCCACCATCATCCTTCGAGAAAATAACTGTCACTTTCTGCGTGTGGACAAGCAGGACTTCAACCGCATCATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022469:ENSMUST00000129223:9
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=0.002
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=FE(29.4=100)
A:
NA
C2:
PF0002724=cNMP_binding=FE(56.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTCAGCCAGGGGGACAAG
R:
GATGCGGTTGAAGTCCTGCTT
Band lengths:
218-391
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