MmuINT0131678 @ mm9
Intron Retention
Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29555706-29556371:+
Coord C1 exon
chr2:29555706-29555826
Coord A exon
chr2:29555827-29556187
Coord C2 exon
chr2:29556188-29556371
Length
361 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
TCCTTTCCATTCCTTCCAAGGAC
3' ss Score
8.47
Exon sequences
Seq C1 exon
TCCACCAGCATTACCACCCAAGAAAAGGCAGTCTGCTCCATCCCCCACTCGGGTGGCTGTGGTAGCCCCAATGAGTCGGGCTACCAGTGGCTCCAGTTTGCCTGTTGGAATCAATAGGCAG
Seq A exon
GTAATGAAGTCCTGGTTCTGTTGGGCGACTAGAAATGGAGTTTTTTGAGGCTTGTGTCCGAGTGCTGGAAGTCGCCTGTAGTCTTTACACCCACTATTACTCACATCTAGAGACTTGTGGGAGAGCAAACCATAGCCATCCCTCTTCCCTCCATGACATGGGCATCTCCCAAGGGCATCCCTGTTGAAACACTCACACTCCTCCCGGTTCCTTTCCTGTCGGATCCGATCCTACACTGGCATCAGAAACGGCCTCGGAGCTAGGCAGGCTTTCCTCTGAGCTAGTGAGCATGTCAGTTGCTTGTCCCTGGTCTCTGCTGTCTTTCCAAGGATGACTGAAGTTCCTTTCCATTCCTTCCAAG
Seq C2 exon
GACTTTGATGTTGAATGTTACACCCAGAGGCGCCTGTCAGGAGGCAGCCGCTCCTGCGGTGGTGAGTCTCCTCGCCTGTCCCCCTGCAGCAGCACAGGCAAGCTCAGCCGCTCAGACGAGCAGCTGTCCTCCCTGGACAGGGATAGTGGGCAGTGCTCACGGAACACAAGCTGTGAAACACTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844-Rapgef1:NM_054050:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.941 A=NA C2=0.774
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCACCAGCATTACCACCCAAG
R:
ACAGCTTGTGTTCCGTGAGC
Band lengths:
294-655
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: