MmuINT0131815 @ mm9
Intron Retention
Gene
ENSMUSG00000038020 | Rapgefl1
Description
Rap guanine nucleotide exchange factor (GEF)-like 1 [Source:MGI Symbol;Acc:MGI:3611446]
Coordinates
chr11:98711243-98711495:+
Coord C1 exon
chr11:98711243-98711293
Coord A exon
chr11:98711294-98711407
Coord C2 exon
chr11:98711408-98711495
Length
114 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
CCTTCTGTTTGGAATGCTAGGAC
3' ss Score
5.44
Exon sequences
Seq C1 exon
AAGCTGCCAGGGAAATTCAAGAACCTGTTCCGTAAATTTGAGGGCTTGACG
Seq A exon
GTGAGTGGAACTGCGTTGTTTTCTCAGCCCCCAGGGAATGGGAGACGTCTTTGGGGTGGGGGGTGGGGGTACATCAGGCCCATTTGTCTCTGAACCTTCTGTTTGGAATGCTAG
Seq C2 exon
GACCCCTGCCGGAACCATAAAAGCTACAGAGAAGTCATCTCCAAAATGAAGCCCCCTCTGATTCCGTTCGTGCCCCTGATCCTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038020-Rapgefl1:NM_001080925:11
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=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=FE(8.6=100)
A:
NA
C2:
PF0061714=RasGEF=FE(15.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTGCCAGGGAAATTCAAGA
R:
CTTTGAGGATCAGGGGCACGA
Band lengths:
138-252
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: