MmuINT0131670 @ mm10
Intron Retention
Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29735984-29736669:+
Coord C1 exon
chr2:29735984-29736085
Coord A exon
chr2:29736086-29736571
Coord C2 exon
chr2:29736572-29736669
Length
486 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
AACTCACCCTTCTCTTGCAGGGC
3' ss Score
10.18
Exon sequences
Seq C1 exon
CACCTGCGCAAGCTCAACAACTTCAACTCCTACCTGGCCATCCTCTCAGCACTAGACTCGGCCCCCATCCGCAGACTGGAGTGGCAGCGGCAGACCTCAGAG
Seq A exon
GTAGGTGGTGGGAAGTCTGGGCAGACTGGAATGGACCTGAGCAAGACCAGGCAAGGATCCCCATCTGGCTCCTCACCTCTGTGTGACCAAGACCTCTGCCTCTCCCACTTCAGATTCCAGTACCTGGAGAAGTCGGCAGGTCCAAGGGCTTTCATGGTTGGTTGTGGGCTTGTTACCTATCCCTGTGCCTGGGTCTCAGCTTCACCTGGAGAGTCCATTCTTTAGCCATTCATCCAAAGTGGCTGCTCTGGGCTTGGCACTGCATTGGGCCTGCTAGGTGGGTTTCATCTAGCACAGTGAGGGCTAGATGAAAGGACAGATGAGCTCCTGAGAAGGGCCTCTCTGAGGACATGTGCTCATACCACCCACAGGATTGTACACAGGCCTGAGACTCTGCCCCAGAGGTTAGCTGACACTATTAGCAGGCGTCCACAGGGCTTTCGTTGGTATCAGGACATATCACATAAACTCACCCTTCTCTTGCAG
Seq C2 exon
GGCCTGGCTGAGTACTGCACATTGATTGACAGCTCATCCTCCTTCCGAGCCTACCGGGCTGCTCTCTCAGAGGTGGAGCCCCCATGTATCCCATACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844:ENSMUST00000102872:21
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=0.015
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=FE(18.5=100)
A:
NA
C2:
PF0061714=RasGEF=FE(18.0=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:
CGCAAGCTCAACAACTTCAACT
R:
GGTATGGGATACATGGGGGCT
Band lengths:
193-679
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