MmuINT0131722 @ mm10
Intron Retention
Gene
ENSMUSG00000022469 | Rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:MGI Symbol;Acc:MGI:2441741]
Coordinates
chr15:97744953-97747129:-
Coord C1 exon
chr15:97747058-97747129
Coord A exon
chr15:97745667-97747057
Coord C2 exon
chr15:97744953-97745666
Length
1391 bp
Sequences
Splice sites
5' ss Seq
CGTGTAAGT
5' ss Score
8.58
3' ss Seq
ATGGCTCTCCCTTCCTCCAGGTT
3' ss Score
11.7
Exon sequences
Seq C1 exon
CGCCTCTATCACCACTCAGAAGCCGAGTGTCCCACATCCACGAGGACAGCCAGGGATCAAGGATCTCCACGT
Seq A exon
GTAAGTGACGGGACAGGGTACTGACAGCTGGCGTAGCTGGACAGAGCCAGACGCTTACGTACGTACATACGCTTACGTACGGACGCTTACGTACGTACAGACGCTTACGTACGGGCACTTTCATACAGTTCGTTGGCGCCTGAATGGGACAGATATCCCCGCTAGCCCAAGCTAAAAGAGAGTGCTGGAGGTGAAGTTCTTGTGATAACTCCATCCTACGTACTTATCTGATGGGAGGTCATGCCGTTATGGAGTAGTCATAGCCGATGGTACCTGGCCTGGGCTTGATATATTCATGCTGATAATACTCTGAACCCGTGGCTCAGTCCAAGGCGGAGAACACAGATGGCGACTTGGTTCTCCGCTGTCCACTGGCTCGCTCTCCGCAGCAGCCACTACGATGAATTTTGAGTTACTCCTATTTTTTATTTTACATTTTGTTTTTTGACTGGTTGATTTTTATTTGAGACGGTCTTGCCTCGTGGCCCAGGCTGAGATTCCAAGCCTGAGCTATTTCCTGTGTTTTCATTAAAAAAAAAAAAATAGCCTTATCTCACACCTGCATGCGTCACGCGTATCACAAGGAACTTTTTTTTCAAGTTTTATTTTTATTGATGTGTGTATACACCTGTGCGTATGTGTGAGGTTGGATGCCAGCCATTTGCATATGAGGACACACCAGGGCCGGTGGGCAGAGAACAGCCTCAGCCTTGGGGGGGGGGGGTCATCCTTGGGCAGCCGCTCTCTCTTCTTTGTGAGACAAGCTCTCACTGGCCAGGAACTTAACAAGTGTCCTGGGCTGTCAGACTGGCCCCAGCGATCTGACTGTTTCAGCATGGGAATTACAGACAAGTTATTAGGACAAGCAGTTCATGCCCTGAGCTATCCCTCCAGCTTTTGTTTGCTTTACTTTTTGGCTTTGCTGGCCTGGAACTCATTATGTAGCCCAGGCTAGCTCCAAACTCCTAAAGATCCCCATGCCTCCACCTCTTGGGTGCTGGAGTCAAGGCACGCACCACCATGCCTGGCCATTTCTTGTTTCTTGAAACAGGGCTTGGAACTCTCCATCCTCCTGCCTCAGCTTCGGAAGCTCCCGGATTATAAACGCGCACCACCATATCCAGTCTGTTTTAGTTCCTTTTGACCCAGAGAAGGGGTACTATGCTGAGATAGATCTTGGTGGGCGGAGGGACCTTCTTTCTTCAGACTTTGCATCCACTGCCCTCCTGACTCTGTGGTGGGAGAGACAGTAGTCTGGGGACTTGGATTGAGAGGATGTGAGGTAGGGGAGGGGAGAGAGCTGAGGCTGCTCCCCGGAGAGAGAGGTAGGCGTGGTGACCTGACCATGGCACCTCTCTCTCTCTTTCTCTGATGGCTCTCCCTTCCTCCAG
Seq C2 exon
GTTCTGAGCAGTCCCTGAGCACCCGGAGTCCAGCCAGCACCTGGGCTTATGTCCAGCAGCTGAAGGTCATTGACAACCAGCGGGAACTGTCCCGCCTCTCCCGGGAGCTGGAACCATGAGGAAGGACTGGCTGGAGCAGGCACTCTCTCCGAGGAAGCCAGAGCCTGTGCAACCAAGAGGTCCAGAGGCCAGCCACAGCTGGGCAGGGCTCTCCACAGAGCGGACTCAAGGCCCTGGAGTGGGCAGTGTCGGGGCAGTTGTCCCTGTGATGACTGTCAGCTATGGAGATCTTTGTTCACGGCCAAGGAAAGGGGGGACATTGAGGCCATGCCGTGGGTAGGAGAGCTGGGAGGTACAGGACTCTGGATCAGTAGAGAGCCCTCCCACCGGGCCTTCTGCGCATCTGCACGTCTGTACATCTGCATGTTTGCAAGTCTGTACGACTGTACGTGCAGCTGTACCATCCAGTGGTCGCCAGGCCTCGTGCTTGTTTTCACTGGGGCCAGTGAGCTCACATCTGCACAGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGCCCTGGGTGGGGCCTTGCCTGGGAGAGGGTGGAGAGTTCTGCTTTTCTCTCCACACATCTGAGATAAACAGCTGGGTGTAGGCAGGGCTGTTGCCTAGAGCGGTGGTCTCAGAGGAGTTGTATTGTTTCCATAAATTAACAAAGATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022469:ENSMUST00000129223:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.600 A=NA C2=0.231
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
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCACCACTCAGAAGCCGAGT
R:
AGCTGACAGTCATCACAGGGA
Band lengths:
346-1737
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