MmuINT0131664 @ mm10
Intron Retention
Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29732827-29733762:+
Coord C1 exon
chr2:29732827-29732919
Coord A exon
chr2:29732920-29733576
Coord C2 exon
chr2:29733577-29733762
Length
657 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CAAGTGCCCTTGGCCCTTAGCCT
3' ss Score
4.03
Exon sequences
Seq C1 exon
GTACGAGAAGTTCTCTCCCTTTGCTGACACGTTCAAGAAGCGAGTGAGCAAGAACACATTCTTTGTGCTGGTTCGAGTGGTGGATGAGCTCTG
Seq A exon
GTGAGTGCCGTGCCCAGGGTCCAAGGAATGGCTGCAGATGGTCAAGCCCGTGTGCATTGCAGCAGGCTGCTAGCAAGCCAGAGGGCTGCAGACTTCCTCACCTGGATCAGACAACCATTACGTTCCACAGACGGCTGCTCGCTGATTCCATTGCTTCATCCCAGCTCTGGGAGTATCAGACCCTACAGACCAAGGTGGGGTGGGGGTTAGGTCTGGAGTTCCTTGTAGAGTGAGTCCCTGTCCTATCTGGGACTCTTCTTACTGTAAGACATGCTCATAGCAGCATAGGGGCCAAGTAGAAGAGGCTGCACCTCCAAAACTCCTGCCATTTCCATACTTAAATTAAGCCTGTTCTGGGTGTGCCGCCTCTGAATCCTTGCCCTCCAGTGGCATCTTGCTCTTGTGTGGTGGCTATATAATGTTAAGGTAAGGAATGGAGGAGCTCAGTGGAGATAACAGCCTTCTACAGACACCTGCCTGACATCTCATCACTGTGTTAGACCAGGAGCTTCTCCAAGGCACAGAGAGCAGCAAGTGTGTTGAGTGAGTTGGCAGGGACCTGTTGCAGAAAGGCCACCCCCAGCACTGTGGAGGCTGTGAGTGGCGTCCTCAACTGGGGCCCTGGCCTGCCTTTTACCAAGTGCCCTTGGCCCTTAG
Seq C2 exon
CCTGGTGGAGCTGACAGAGGAGATCCTGAAGCTGCTGATGGAGCTGGTCTTCCGCCTAGTGTGCAGCGGAGAGCTCAGCCTGGCCAGAGTCCTCCGGAAGAACATTCTGGACAAGGTGGACCAGAAGAAGCTGCTCAGGTGTGCCCATTCCGACCAGCCTCTGGCAGCCAGGGGTGTTGCAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844:ENSMUST00000102872:16
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=0.000
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(31.6=100)
A:
NA
C2:
PF0061815=RasGEF_N=PD(18.4=28.6)
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:
GTTCTCTCCCTTTGCTGACACG
R:
CTGGCTGCAACACCCCTG
Band lengths:
270-927
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