MmuINT0131822 @ mm10
Intron Retention
Gene
ENSMUSG00000038020 | Rapgefl1
Description
Rap guanine nucleotide exchange factor (GEF)-like 1 [Source:MGI Symbol;Acc:MGI:3611446]
Coordinates
chr11:98845875-98846289:+
Coord C1 exon
chr11:98845875-98845987
Coord A exon
chr11:98845988-98846121
Coord C2 exon
chr11:98846122-98846289
Length
134 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
AACCTGTCTCTGTTCTTCAGTTT
3' ss Score
7.96
Exon sequences
Seq C1 exon
GATTCCAGAAGAGAGCCAGCCGCCCAGCAAGCAGGTTAAGCCGCTCTTCCGACACTTCCGCCGGATAGATTCCTGTCTGCAGACCCGAGTGGCATTCAGGGGCTCCGATGAGA
Seq A exon
GTGAGTATGACCCTTAGGAGGAGCAGAGCTTCTGGAGAAGGTCTGGGAGGTGATTGGGTCTGTGGGCCTTTGTGCACCAGCAGCGGAGTCTCCGAAGGCCCTTTCACGGCGTCTAACCTGTCTCTGTTCTTCAG
Seq C2 exon
TTTTCTGCCGAGTCTACATGCCTGACCACTCTTACGTGACCATACGCAGTCGCCTCTCGGCATCAGTGCAAGACATTCTGGGCTCTGTGACAGAGAAGCTGCAGTACTCGGAGGAGCCTGCGGAGCGCGAGGATGCCCTCATCCTTGTAGCTGTTGCTTCCTCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038020:ENSMUST00000107479:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0078818=RA=PU(2.5=5.1)
A:
NA
C2:
PF0078818=RA=FE(70.9=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:
AAGCAGGTTAAGCCGCTCTTC
R:
CCAGAGGAAGCAACAGCTACA
Band lengths:
251-385
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