MmuINT0131709 @ mm10
Intron Retention
Gene
ENSMUSG00000022469 | Rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:MGI Symbol;Acc:MGI:2441741]
Coordinates
chr15:97757350-97757761:-
Coord C1 exon
chr15:97757683-97757761
Coord A exon
chr15:97757510-97757682
Coord C2 exon
chr15:97757350-97757509
Length
173 bp
Sequences
Splice sites
5' ss Seq
CCAATATCC
5' ss Score
-12.74
3' ss Seq
TTCCCTTGACCGGTGTCCACCTT
3' ss Score
-5.48
Exon sequences
Seq C1 exon
AGACGTTCCTCAGTGACTTCCTGCTGACCCACAGTGTCTTCATGCCCAGCACCCAGCTCTTCACTGCCCTCCTGCACCA
Seq A exon
ATATCCTTCCACCCACAGGATGATGTGGGTAAGGGGGTGGGATGGTGTGTCGAGATGAGGGAAGGAATCTCAAAGTGGCCGCCGTATGACCCTTCCCTGGATCCCTGAGCAGTCGGGTCCTGTATGACGGGTGGCCTCAGTGGCTTGTTGTGGTTCCCTTGACCGGTGTCCAC
Seq C2 exon
CTTCCACGTGGAGCCAGCAGACCCTGCTGGAGGCAGCGAGCAGGAGCACAGCACCTACATCTGCAACAAGAGGCAGCAGATCCTGCGGCTAGTTGGCCGATGGGTGGCCCTGTATAGCCCGATGCTCCACTCGGATCCCGTGGCCACCAGCTTCCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022469:ENSMUST00000129223:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.241
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(23.0=100)
A:
NA
C2:
PF0061815=RasGEF_N=FE(46.9=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:
CGTTCCTCAGTGACTTCCTGC
R:
CTGGAGGAAGCTGGTGGCC
Band lengths:
236-409
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