MmuINT0131705 @ mm10
Intron Retention
Gene
ENSMUSG00000022469 | Rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:MGI Symbol;Acc:MGI:2441741]
Coordinates
chr15:97766762-97767798:-
Coord C1 exon
chr15:97767395-97767798
Coord A exon
chr15:97766975-97767394
Coord C2 exon
chr15:97766762-97766974
Length
420 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CTTTCCTCCCCACATCACAGGTC
3' ss Score
9.01
Exon sequences
Seq C1 exon
ACCCCTACCGTAAAGCTCGTGCCTGCTCCCCGCCCCCTCGGCCTGTCCGGGGAGGGGAAGGGGCGGGCAGCGCAGGGGGTGTGACAGCTCCCGCCCGGACCAGTGCCAGCTGCAGCTTCGCTTGAACGCCCTGTGCCAGCTGGCTCTTACATCTGGGACGGAGGCGGAGGCTTGGAGTTCTTAGCCTTTGGGAAGGGGTGGGGGCTGCCCCACACCCCCAGCCCTCTATTCACCCAGGACAAACCCTATCTGCCTAGCCCTGCATCTTGCTGCTCCAGGCAACCTGTCTGACTAGGGGCTGGCCCTTCGCTGCATCTCGGGACTCACACTCATACCGCTCCAGGGATCCTGCAGCCTCTTGCTAGGGCGAGCACCGCGGTGTGAGCTGGAGAAGAAACATGAAG
Seq A exon
GTAAGGTGGGCCGGAGTCAGGGCCAAAGAAAGCTGCTGGAAAGGGCGGGAGAGGAAGCCGACACGTGGGGGAGTTTGGGTGGGAGAGAGTGGCGGGGAGGAGAATTTGAGGAAAAGCTGCTTCTGGGGATCTAGTGTGTGTACAAAGGTGGACATGCCTTCAGGACATGGGTAGTGAGGTGGGGCCGAATTCCAGCCAGAACTGAGAAGAGCCCCATCGTTGTGAGTTGAGTGGAGACCCCTAGGTGCGCCAAGCCAGCAGGACCCGGGGCAGGTCTTCCTGTCCCTCCCCCGGCTCCTGGCAGGGTTGCCGCACCTCCGCATGACCAGTCCAAGTCCAGAGGACGCTAAGCCAGGGGTGGTAGTGGGGAGGTCCAGCTCCTCCGGCCGATGGCTGTCCTCTTTCCTCCCCACATCACAG
Seq C2 exon
GTCAGCTGGCCAGGTGAGAACCACTGGCAGGTGGGCCCAGCTGTGGTGGAGAGTCCAGCTGTGGGGGCACCGCAGGTGGGAGGTCTCCCGGACGTGGTTCCGGAGGGCACGCTGCTCAATATGGTGTTGAAGAGAATGCACCGTCCCCGCTGCTGCTCTTACCAGCTAGTGTTCGAGCACCGGCGCCCCAGCTGCATCCAGGGACTCCGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022469:ENSMUST00000129223:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.143 A=NA C2=0.071
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACCCTATCTGCCTAGCCCTG
R:
CGGTGCTCGAACACTAGCTG
Band lengths:
345-765
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