MmuINT0131666 @ mm9
Intron Retention
Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29589720-29590039:+
Coord C1 exon
chr2:29589720-29589804
Coord A exon
chr2:29589805-29589944
Coord C2 exon
chr2:29589945-29590039
Length
140 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGA
5' ss Score
8.55
3' ss Seq
CATGTTCTGTTTCTACACAGATT
3' ss Score
10.7
Exon sequences
Seq C1 exon
GCCAGGAACCTTGCATGATTTCCACAGCCACGAGATAGCTGAGCAGCTGACACTGCTGGATGCCGAGCTTTTCTACAAGATAGAG
Seq A exon
GTATGACTGAGTGGTCCTGCAAGGGAGGCAGCTAACACTCTGCCTGGAAGCTGCTGCTGCTGGCTGTGCCTATGGAGAGCCCCACACCCAGACCCTGGAGCACCAGAGACTGCAGTGCTGCATGTTCTGTTTCTACACAG
Seq C2 exon
ATTCCTGAAGTTTTGCTTTGGGCCAAAGAGCAGAATGAGGAGAAGAGTCCCAATCTGACCCAGTTCACAGAGCACTTCAACAACATGTCCTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844-Rapgef1:NM_054050:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.094
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(12.9=79.3)
A:
NA
C2:
PF0061714=RasGEF=FE(17.4=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:
GCCAGGAACCTTGCATGATTT
R:
AGTAGGACATGTTGTTGAAGTGCT
Band lengths:
179-319
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: