MmuINT0131668 @ mm10
Intron Retention
Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29679133-29679850:+
Coord C1 exon
chr2:29679133-29679269
Coord A exon
chr2:29679270-29679736
Coord C2 exon
chr2:29679737-29679850
Length
467 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
CCAGGTTTCCTCTCTTCCAGGAG
3' ss Score
9.2
Exon sequences
Seq C1 exon
ACTCTCAGCGTTCTCATCTCTCCTCCTTCACCATGAAGCTGATGGACAAATTCCACTCTCCCAAAATCAAGAGAACACCATCCAAGAAGGGAAAGCCAGCCGAGGTGTCGAAGATTCCTGAGAAGCCTGTGAGCAAA
Seq A exon
GTAAGCTGCGCCTCTAAGTGTTCCTCCTGGTCCCAGCCTGCGGCCAGCGTTGTGAGCTGCACTGGCTCTAAGTGCACTCACTGGGGCCATCTGTGTCCCTGGGACCTGGGACCTCTAGGACTGCTAATCAGTCCGGCCAGTGGCTTGGACAGTTTCGTGTCATCCTCTGGGCATTTAAAGTAACTCAGAGCACTGTGCTCACACCTGGTGCTGCCTCCCACCCAGAAGCCCTCGGGTACTCTCACACAGGGCTCTGATGGCCTGGACCAAGCGTTCAGCCTCAGGGCCTGGGCTCTGAAACTCACAAGCCCCTGAATCCCATCTAAAAGCATCCTCCAGCATTAGTAACCTCAGCAGGGCCAGCTGAGCCAGATGTGTGGAACAGCTGTTGATTCTCACCAACCCCTCCCTCCAGTCTACAATGTCCATTTCAAGCTCTGTAGGAATCCAGGTTTCCTCTCTTCCAG
Seq C2 exon
GAGGCAAGAGACAGATTTCTACCAGAGGGCTACCCTATCCCCTTGGATCTGGAGCAGCAGGCAGTAGAATTTATGTCCACCAGTGCTGTGGCTTCCAGGTCTCAGAGGCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844:ENSMUST00000102872:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.527 A=NA C2=0.105
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CAGCGTTCTCATCTCTCCTCC
R:
CTTCTGCCTCTGAGACCTGGA
Band lengths:
246-713
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