MmuINT0131821 @ mm10
Intron Retention
Gene
ENSMUSG00000038020 | Rapgefl1
Description
Rap guanine nucleotide exchange factor (GEF)-like 1 [Source:MGI Symbol;Acc:MGI:3611446]
Coordinates
chr11:98842558-98845987:+
Coord C1 exon
chr11:98842558-98842655
Coord A exon
chr11:98842656-98845874
Coord C2 exon
chr11:98845875-98845987
Length
3219 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGG
5' ss Score
4.44
3' ss Seq
CCCAGCAATGCTCATGCCAGGAT
3' ss Score
1.71
Exon sequences
Seq C1 exon
GAACTGTATCTACTAATTATGAAGGATGAGTCTCTTTACCAGGACCTCCGAGAGGACACACTGAGGCTACACCAGCTGGTGGAGACAGTGGAGCTAAA
Seq A exon
GTGAGGAGAAAGGGGACCCCTGAGTTCCTCTAATACAGGGGCTGCCTCTGGTCTTGTGGCTTCAACATATCAGTTATTTGTTTCTTTGCTTGCTTGCTTTCTAAGCTATTTATTTATTTATATTGCTTTATCTGCATGTATATCTGTGTACTACCTCCATGCTTGGGTATGCCAAGGTCAGAAGAGGGTTCCCAGGAACTTAAGTCATAGATGGCTATAAGCTACAAAGTGGGTGTTGGGAACAAAATGGGGTCCTCTCTGCAAGAACAGCCAGTACTCTAAATCACGAAGCCATTTCTCCGGCACCTTTAATATTTCAATATGATTTTCTTTCAGCTCTTTTCCCTTATTGGAGAGTAACATAGAATCACACAGAATGATGTCTCTAAATCAATGTATTTTTAGAGGGGCAAGGAAGGAGCTGGGCAATGTCTCTTACTTACTCTATAGCTCAAGCTAACCTCCAGCTCAATTTGTAGCCCAAGACGGCTTCTGCCAGCAGCAATCCTCCTGTCTCAGGGTTCCGAGTGGGCCTGTGCCACCAGGTCCAGCTCCATTCTTTTAGTTTTTGGTCTGCTTTTCCTATTAGTTGGGTAGTGTTCCAGCAGGTATTTAACAGCCCCTGCTTTCTGGGAAAGAGCCCAGTTTTCTAGTTTATAGCTCTGATTCCCATGGCGTAAATTTTCTCACCATGGTTTGTCTCAAGCTATCAACATGGTATCCTTGACTGTGGAGTTGAGAAGAGATCTGCAGTAGTTACATAGTATTTCCACTACCTCCACAGCAGGCCTGAATAAGCTGGAGCAGAGGCAGTACAAAACTTAGTAAAAAGAACTTAGAAAAACTACCTTTTGGGTTTTTTCCCCCTCTTCTTTCTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTGGTTTTTTGAGACAGGGTTTCTCTGTGTAGCCTTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTTGAACTCAGAAAATCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTGAAGTCGTGCGCTACCATACCTAGCTTTTCTTATTTATTTATTTACTTACTTTTCAGATGGAGTCCTTGAAACTTGCCCCAGTTTTTTTTTTTTTTTTTTTCACATTTGCCTCCTAAAGTCAAATTATAGGCTTTTCCATGGTGCCTGGCACAGGTTTTGCTATGTTTTGTTTTGTTTGTTTTCTGAGACAGGGTTTCTCTGTGTTCTTAGAACTCATTCTGTAGATCAGGCTGGCCTCAAACGCACAGAGATCCACCTGTCTTCTGCCTTCCCAGTGCTGGGATTAAAGGCATGTGCCACCACTGCCTGGTGAAGCTGTCTTTTCAACAATGATTTATTTGACCTTAAGTTTATAACAGGTGCCAGGCGGTGGTAGCGCATGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTAGATTTCTGAGTTTGAGGACAGTCAGGGCTACACAGAGAAACCCTGTCTCGAAAAACCAAAAAAAAAAAAAAAAAAAAAAAGTTTATAACAGGTGTATGTATGAATGAATACGCATCCAATGGCTGTCCTTAAATTTTAGCTAACATGAGTGACAGAGATGGTTCAGTGGTTAAGAGCACTTACTGCTCTTCAAGAGGACCCAGGTTGCATTCCCAGCACATGGGCTCACAACCATCTGTAAGTTTAGTTCCAGAGGCTCTGATGCTCTCTTATACACTCTAAGTGTAGGGCTTGCCATGGTACACAGGGCACATGCAGGCAAAAATACCCATACGCATTAAAAACGTATTGGTCGATAGCTGAGCGTGGTGGCGTATCCCTGTGATCCCAGGTATTTGGGAGGCTAAAGTGGTAGAAGAATCATCAGTTCAAGGCCAGCTTGGACAACTTAATGAGATCACATCTCAAGATTCGAAAAAAAATAGTAAGGGCTTGAGACACAGCAGTGGTGCAATGCTTGTCTAGTATGTGTGGTGTCCTAGGTTTAATCCCCACTTTTACCAAAACAAACAAACAAACAAACAAACAAACAAACAAACAACAGTTGGCAAAAATCCCCAGAATTGACCTCCCTAGCATCAGGACACGAGTGCATCAAGTCATCCCTTGGTTTTCTCTGCTCCATTCCTGCTGCTACACGGTTCATTAACTCCCCTAGGCTGTTGCCACAGCCTGTTCGGGACTTCAGCCTCTGGCCTTGCCTCTTTCTCCCTTCTGACACCAAAGGTATCTTGCAGACTTTCCTAAAGGAGTCTTTCACCTCCCTGTTCCCAAAGCATCCGTTTTCTAATGTCTCCAAGCCAGCACCAGCATCCTTCCCTTCCCACCACCCGATCATCTAAATATCCTAAGCCACCATCAGCATCCTTCCCTTCTCACCACCTCCTGATCTTCTCTGACTCCTCTCATGTTTCCTTTTCACCTATTTTTTAAATTTATTTTTATTTTATGTACATTGGTGTTTTGCTTGTCTGTATGTTGGATCCCCTGAGGGTGGAGTTGCAGGCAGTTGTAAGGTGCCATGTGGGTGATGGGAATTGAACCCCGGTCCTCTGGAAAAGCAGCTGGTGCTCTTAACCACTGAGCCATCACTCCAGCACCCCCTCTTCATCTATTTTTCTGGCAACTTTGGTGCCTTCCTACTTTTTCTTCCCATGATCCTTCAGGGCTCTGGTCAAAGGCCGTCTCTTTTATGGAAACACCTCAGATTTCTCCCTTTCAGGAACTTTCCTTCCCCCACCCACAAGTCTCCCCCTCCTGCACCTTTGTCACCTCACCAACACTTCCTGGCTGGTGTAAGAAGTAGCTGCAATGTCTGTCTCCTTCACAGACTGTGAAACCCTTGTCAGCAAAATTCAGGCATCTGATGTCCTACTACCTACCCTGTGCTGAGTGTGGCAGGACATGAAGGGTGAAGGACTGTAAAAAATAATCCCGTTCCCCAAGAGCTGTCAATCTGGTAGAAAAGACGACACGAACCCAAACAATATTGTTCCATCATTTTATGGCTTTTGAGACGAGTCATCTTTCCTCATGGGTGGGTGGACCAGAGAAGAGCCCCTGAAAGAGGTGGCATTTGATCTGGGCCACTTGGACAGTTGTCCTGTGCTGGTCATTGTCCTACCCCTGCTTAATGTTCCTGCCTGGTGCTCCATATGCCTGGCAGGGCTTGCTGATGCCCAGCAATGCTCATGCCAG
Seq C2 exon
GATTCCAGAAGAGAGCCAGCCGCCCAGCAAGCAGGTTAAGCCGCTCTTCCGACACTTCCGCCGGATAGATTCCTGTCTGCAGACCCGAGTGGCATTCAGGGGCTCCGATGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038020:ENSMUST00000107479:4
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=0.077
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0078818=RA=PU(2.5=5.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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