MmuINT0131707 @ mm9
Intron Retention
Gene
ENSMUSG00000022469 | Rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:MGI Symbol;Acc:MGI:2441741]
Coordinates
chr15:97588448-97588934:-
Coord C1 exon
chr15:97588822-97588934
Coord A exon
chr15:97588537-97588821
Coord C2 exon
chr15:97588448-97588536
Length
285 bp
Sequences
Splice sites
5' ss Seq
CCGGTAACA
5' ss Score
5.92
3' ss Seq
ATTTACTGTTTTACCCCTAGGTA
3' ss Score
11.61
Exon sequences
Seq C1 exon
GATGTGGAAGCAAAAACCATGAGACTGGAAGAACACGGCAAAGTGGTCTTAGTTCTGGAGAGAACCTCTCAGGGTGCTGGCCCTTCCCGTCCCCCGACCCCAGGCAGGAACCG
Seq A exon
GTAACAAGCCTATCATGTCTCTTCCGACACAGCTCCACACTGCCCTACCCAGTATGCTTCTTGCACCTCCAAGCCTTGCTCTGTTTCCATGCCACGCTGATGCCCTTTGCCCATCTGGGGGTGGGAGACACTGAGAGACTGAGAGGATAATCAATGCCCCCTCTCCAAGATGGAATAGGGCTAGCCAATCGTAAGGTGTGATGTAATCAGTTATTGATGTCTGTGTGCAGAGGTGGGGGTGATGTCCTTAGGGCACATGCTATCAATTTACTGTTTTACCCCTAG
Seq C2 exon
GTATACGGTCATGTCTGGCACCCCAGAGAAAATCCTAGAACTGCTGTTGGAGGCTATGAGACCGGATTCCAGTGCTCATGACCCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022469-Rapgef3:NM_144850:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.579 A=NA C2=0.290
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(2.4=5.3)
A:
NA
C2:
PF0061815=RasGEF_N=PU(24.8=90.3)
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:
GGAAGCAAAAACCATGAGACTGG
R:
CTGTTGGGTCATGAGCACTGG
Band lengths:
197-482
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: