MmuINT0131667 @ mm10
Intron Retention
Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29734425-29735880:+
Coord C1 exon
chr2:29734425-29734519
Coord A exon
chr2:29734520-29735801
Coord C2 exon
chr2:29735802-29735880
Length
1282 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
TACCTGGTCCTTTCCTGCAGGGT
3' ss Score
10.71
Exon sequences
Seq C1 exon
ATTCCTGAAGTTTTGCTTTGGGCCAAAGAGCAGAATGAGGAGAAGAGTCCCAATCTGACCCAGTTCACAGAGCACTTCAACAACATGTCCTACTG
Seq A exon
GTGAGATGGGGCCGCAGCACTTGGCTCGGTGGTGTGCGTGGGACAGTTGAGACTTCCTTGGCAGAGAGGTCAAGTGGTCAGTCCTTGGATATTTCCAGAGTCTGTGGGCACTAGCCTTGAACTGTGGGCAGCAGAGAGAAGGAGGCAGACAGAGCTGGCTGAGGTGGCACCATAGGCTCTGCCGTGCAGGGAAAAAAAGTGCCAGGATTGATTAGTAATGTCTGCCCAGGCTGGAGGAGGTACCCTTCTATCGTTGTTGCTCATTGCCTCTGCAGTTCCTGTAAGACATTAGCTCACCTGATTGCTTGATAGAGACCAACTGCTTAGCAAAGGAGTGGATTGTTAAGGCTTTGATTTGTACCTGAATTCTTTTTTTTTTTCTTTTGCGGGGGGGTGGGGGATGGGGGGCGGGGGGGTGCTGTCTCTACATAGCCCTAGCTGTCCTTGAACTCAGAGATGGCCTGCCTCTGCCCCACAAATGCTAGGATTAAAGGTGTGCACTACTACCTAGCTTGTGTCTGAATTCTTAAAGCAGAATGGAGGTCAGCAGTGTGTCTATCACCTGGTCGCTTTGCCATTTCAAGATTAGACCAGGTACCTCCACCTCCTACTGCACTGACCCTGCCCCACATGCCTGCCATGGCCCTAGGGAAAGGTCTCATTGCTTCTCTGTGCTCTTGGCGGGAAGCACCGGCCCCTCAGCAATAACCACCACTCAGTCTGAGTGTTCTGGCTTCTAGGGCCAATAGGCAGTACTTACCTTTTGGAGCCATGGTCTCTGACATGTCCCTGACACAGGTGCTCTTTACGGGATAGGAGAGGTGATTAGAGTATCGCACCTCACCCCAAGTAACACTACAGTGGCCCTTGTAAACCACAGAAGACTGAAGCCACCCTGAGGTCAACAGAAGAACATGAGGCTTGCCTGGGCTTCAGCCTCCATTACTGCTAAGGTCCTGAGTCTCCATCTCCCATTGACTGGCAGAGTGGTCTCCTACTCCTCTGTCAGCTGGGATCTGAGCCAGCAACAAGGCCTCATAATGCCTCTCTCTGCTGAAAGATGCTCCAGTCCCCAAGCCCCCTCTGCAGAAGAACTGTCTGGACCCTAGAATATAGTACACACCCTGAGATCAGGGCCAGGGTCATGCTTGGGCTTTGGGCTCCTGGTGGGTAAGAACTTGTGACAACTGGCACGGGAGTCACTCACATTTCGTCTGCCAGGGCCACTGAGCCAGTGGAGGATGGTGAGCTCAGCTGTTGCTTACCTGGTCCTTTCCTGCAG
Seq C2 exon
GGTGCGGTCCATCATCATGCTGCAGGAGAAGGCCCAGGACCGGGAGAGGCTGCTCCTCAAGTTCATCAAGATCATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844:ENSMUST00000102872:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.094 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=FE(17.4=100)
A:
NA
C2:
PF0061714=RasGEF=FE(14.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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