MmuINT0131824 @ mm10
Intron Retention
Gene
ENSMUSG00000038020 | Rapgefl1
Description
Rap guanine nucleotide exchange factor (GEF)-like 1 [Source:MGI Symbol;Acc:MGI:3611446]
Coordinates
chr11:98847076-98847409:+
Coord C1 exon
chr11:98847076-98847173
Coord A exon
chr11:98847174-98847286
Coord C2 exon
chr11:98847287-98847409
Length
113 bp
Sequences
Splice sites
5' ss Seq
CTAGTAAGA
5' ss Score
5.2
3' ss Seq
ACCCCCCCACCTGCCACCAGGTA
3' ss Score
8.76
Exon sequences
Seq C1 exon
AGAAGGTCCTCCTCCAGCCAACGGAGGACTGCGTTTTCACCACGCTGGGTATCAACAGCCACCTATTTGCCTGTACCCGGGACAGCTACGAGGCCCTA
Seq A exon
GTAAGAATCCTTTTACCCGTCTCTGCTGGTAATGAGAGAGGCGAGAGGCGGGGCTGAGTCTCTCACCTTACCACTGGGAGCCAAGTTCCTCTCACCCCCCCACCTGCCACCAG
Seq C2 exon
GTACCCCTTCCGGAGGAGGTCCAGGTCTCCCCAGGAGACACAGAGATCCACCGGGTGGAGCCTGAAGATGTGGCCAATCACCTGACTGCTTTCCACTGGGAGCTCTTCCGATGTGTGCACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038020:ENSMUST00000107479:7
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=0.146
Domain overlap (PFAM):
C1:
PF0078818=RA=PD(25.3=60.6)
A:
NA
C2:
PF0061714=RasGEF=PU(13.0=58.5)
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:
GAAGGTCCTCCTCCAGCCAA
R:
CTCGTGCACACATCGGAAG
Band lengths:
220-333
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