MmuINT0131662 @ mm10
Intron Retention
Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29726206-29730612:+
Coord C1 exon
chr2:29726206-29726281
Coord A exon
chr2:29726282-29730527
Coord C2 exon
chr2:29730528-29730612
Length
4246 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
ACTGCTTTGCACCCCTGCAGACC
3' ss Score
9.47
Exon sequences
Seq C1 exon
GGTGATGATGGGCCAGATGTTCGTGGTGGTTCAGGAGACATCTTACTGGTCCATGCTACTGAGACAGACAGAAAAG
Seq A exon
GTAAGGCAGCTCCCACTGTGCTGGATTGTGTCCCACCAAAGGCATCACATGACTGCACTGTACTGTCATCTCTCCTGGGTTCAACTTTGGATCTGATGGTACCAGGAAAGGGTAGGGAGAGGCCGGCTCCAGAGACCCTGATGCTGTCAAAGTTGCTCCTGGGCATGTCCCCTCTTGATGCAAGATGATGATGCATCCTGAGTGTAAGAACAGTCATTGGCACCTACTGTGTGCTCCAAGGGCAGCCCACTGGATAATGACATGTTCAACCGTGGCATTAAAGGTAAAGCAGCCACAGTAGTCCATACCTAGGATCCTGGCACTCAGGAGGCTGATAGAGGTGAATCTGGATTCAGACCAAAAAAAATCTTCTACAGTAGCACATGGCCCTCTGCCTTTCCTTATATTTAGGTCATTCTTTTCTTCAAAGTCTTTAGTTCACATAGTTAACTAACAAGTTCCTAGGAACAAAATTTGTTGTCCAAAACCTGCCCCAACCTTGCCATCCTCTCTGCATCCTGATCATCTGAGCAGGAGGAGAAGCAGAGGCTGTACCTAGACTTGTTAAGTAGGCTGTGCCCGCAGAAGAACCATCCATCCACGAAGTCCTGTAAGGGAGATTGGGCTCCCCTGAGCTGCTCAGGCAAGGCCTGCTGCTGCTCCGCCCCAGGAGGCTAATGAGCCCACCTCACGCCACAGCCAGTTTCTTGTTAGTATTCCTTTTCTTTCTTGTCTGTTTTGAGACAGAGTATGTGTTCCATGAGCCCTCTTCCTACACATTTTTAAAGGATTTAAAAGAAGCAGAGCATCCTCACACGTGCCTTTAATCTCAGAATTTATGAGGTTCCAGGGCTGTATGGAGAGACAATGTTATAAAACAACAACAGAAAGCAGAGCTAGGCTTATGGCTCAATGAGAAAACACTTGCCTAGCCATGAATGAGGCCGTGGAATCAATCCCCAGCACTTGGGAGGCAGAGCCCTCCCTGTGAGTTCAAGGCCAGCCTGGTCTACAGAGGGAGTTCTAGGGCAGCCAAGGATACACAGAGACACCCTGTCTTCAAAAAAAAACTAAAAGAAAAAGAAAAGAAATTCTGAAAAGTTGATTAAACTGTAGATAAAATCACTCCAGACTTAAAGCCCTAACCCAATCAGCTTTCTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGAAATGTCTAGGACCCAAGGGTCTATGAAACTCTAAATTAAGAGAATAGTACAAAAACTGTTTGCCTGACAGAAACGGAAACAGGTTTACCTTCATCTGAGCCCTCAGCGATTCTTCACCCATTTCCTCCAGCCATGACAAGAAGGGAGTCTCAGACACTCAATTTGAAGCCTACCTTAGCCTTGCAGCTACGGGACCGCCTTTCCCCTAGGGCCTTGGTTCCAGGGGTACAGACAGTGCCCAGTGTTCAGTGGCACCTCAGGACATCCTGGCAAAGTAGCCATTTTCACCTCATTTTTATCTAAAAGTGAAAGTCTAGGATGTGAGCTGGCTTCTGGCCTGGTCATGTAAGGATTTGCCCTGCCAGCTGCTGCCAGCTGCTGCCAGGCCAAAGAGCTCTCTGACAGGGAGCCTAAAGGCCTTCTGGTCTACCCATTGGGTATGCTGAAGAGAGACTTTTGAACTGAAGTTTCAATAGGATTTGAGGTCCCTGCAGAACCAGAGTTGGCTTTACCTGGGAGTCTTACCTGAAACAGAGGCCGTGAGCCACATCAGAGTGGACATGGTGCCCATAGAAGATGGCAAAGTTTGTCAGGCAGGGGGCTTCCTGCACCAGTGGTATATGTGTGACTCAAAGGTCCTGGGAGGCTTCATGGCTCATATGTCTAGGACTCAGCTGTGTCAGACAGGGCCAAGCCAATTAGACAAGTAAACAAGAAGGGCACACTTGTCGTAATAGCCTTTCTCTCAGGTGGCTCTGTGAGAAGTGTCAGAGGGCCAGGTCGGGGATAATGTTAGGCCCAAGCTCAGATCCTGTCCCTTCCTTGGGACCTGTGTCCTAGACCTGTTACTTGGCCCCCAAGCTTCCATTCTTCTGAAGGCCACTGGGGACAAAGGGACCTGAACTAAAACAGCCCTGTGAATTTGACAGACAGCCCTGTAGCTTTTGGCTCAGGCTCCCACCCAAATGCCAGGCGATACCAGAGCCCACAGATAGGTTATGCAAAGAGCTCTAGTACCAGCAGGCCTGTGCTGTGTCTGGCATGGCACAGCACAGCCATCCTTGAGTCTGGTGTACTCTCCTCCTTCTCCCAACACGCGCGCACACACACACACACACACACACACACAGGCTTTCTCTGTAGCCCTAACTGTCCTGGAACTCACTCTGTAGACCAGGCTGACCTCAAACTCAGAGGTCTTCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAAGTGTGTTCCACTGCTACCTGGAATGTCTGGCCTACCCTTTGTCTCACACATAAGTTTCTTTACCTTCCAGCCTGTGAAGTACGGCTATAGTGCTCACCAGCACACTAGAACACACCCTTCAAGAGGTCACAGGCTCCTGCAGTGCTCCTCTGCGTTTGTACCCCTTGTATGCCCAACCTCTGCTCTTTCTAGAAAGTTCCAACGTAACAGGGAGTTGGTTAGAATACAACTTTGAGGCTGAGCACAACTCAGGGACCAGGCCCCCCACACCTCAAAGGTGATGGCACACAGTGTGATGGTATGACGTGCCACACAGAGCCTTGAGCCCCCTCTATTTTGGGAAATATTAAAAAGATCATCAGCAAGTTCCCAAGTTACACCCAGCTACTCTCAGCCCCAGCAGTCTCTCTAGCCAGTTCTTATCTCATGGAGACTTTCTGACTCAGAGCTCCAAAATCTCTCTACCCAACTCGCTAAGTTCTCACTGGCGAGTCACTACCATGCCAGCCCCACACTTCAAAACTCCCATGGCCTTTGTGGTGCACATCTGGCAAACCCACACTCTGCCACCATACCTTTCTCCCTTTCTCTCTTGAACCCAGTCAAACCACTGGGTGAAGGAAAACACCACATAAACTTAGTTCAGAAACAGTGGTAACTCAATCACTGGGCACAATAACTAGAATCCTAATCTTGTAAGCCATGTTAAATCTAAATCCTCTGGTGGCAGATCCTGGTGGATGCACCATGGAAACCAGGAGACACTCGAAGCTCTATCTTGCCCTCTCACTATCCAGTCCAAAAGGACCCCACACACACACCCTTTCCTCTCTTCCCCTATCTAACCCAGAAGTCCCTCCTACTCACCCAGTGATTGGCTCATTTATTCATTAGGGGATGGTTTACAAGAAGTCACCTGAGTTCCTGACTTACTCCTTGTTTGAAACCCCTCCCAGGGGAGCAGAATTAACATCAAAATACAAACAGCATCAGGCCCATCCACAACACCCCTCCATCCCAGCACTTGGGGAGGTGTGAGAAAGGGCAAGGGGGCTGCTCTCCACCTCCACGTGGTGACCTCCTTTCTAGGTCCAGTGTGGTGCAGTACAGCCCTTCCTGAGTTAGCCCACCTTGTCTCTCATGACATCCTATGCTTAATATCTAAAGCATTCGGGAAATAAGTCACAACAGCCAACAGGGCTCTAGAGAGGCGGGACTCATTAACTGGCATACTCTTTCCCTTTGGAAGGAAGAGGTGGGTGCTACCAGTCTGAGGCCTCCAGCTATGGGGGTTCTGTGTGTCACCACTGCCCTTGCCCTGTGTGGGCAGCAAACCACTGCTAAGCTTTGCAGTACACCACCACTTCAGCCTCCCCTTGAGGCTTAGAATGGAATTTCCCAAAAATATTTAATGACTGGACCCTGTTATCTAAAAATACTGCCTCTGGTTTAACTGCAAGAGCCTGTTGGCAAGTTTGGACAACTATCTCTGCCCAAAGCAGTGAGGAGCCATTGAGCCACTGGGCCTTAGGGCAGCATCTGTGCTAATCTGTGGGTGGTGCAGTCCAGAGCCAGTATGCCCAGGCCTTGACCTCTTACCAGCACAGGGGTCACTGAAGAAATGAAGTTTGTTTCCTACACTGGGCCTCAGGCCCTCCCACAGCTAGGTTCTCCATCAGAAGTAGCCAGTGCCCATAAGATGAAAGACCTAGGACCTACCTGGCTTTTAGAGAGGACTCAGCATGGTGCCTATGCTGTGAGCCACAGCCACACCTACACCCTGAACCCTACCACCCTGACTGCTTTGCACCCCTGCAG
Seq C2 exon
ACCTGGTGCTGTACTGTGAAGCCTTCCTGACCACCTACAGGACCTTCATCAGCCCGGAGGAGCTCATCAAGAAGCTGCAGTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844:ENSMUST00000102872:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.462 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=PU(20.4=76.9)
A:
NA
C2:
PF0061815=RasGEF_N=FE(28.6=100)
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:
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