MmuINT0131673 @ mm9
Intron Retention
Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29535257-29541803:+
Coord C1 exon
chr2:29535257-29535370
Coord A exon
chr2:29535371-29541624
Coord C2 exon
chr2:29541625-29541803
Length
6254 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
AACATGGCATTCCCTTTCAGAAC
3' ss Score
8.09
Exon sequences
Seq C1 exon
GAGGCAAGAGACAGATTTCTACCAGAGGGCTACCCTATCCCCTTGGATCTGGAGCAGCAGGCAGTAGAATTTATGTCCACCAGTGCTGTGGCTTCCAGGTCTCAGAGGCAGAAG
Seq A exon
GTCAGTGTGACATTAAGAACAATTGGGGTTGCCTTGCCTTCCACTGCAGAACTCTGGTCCGTGGTCTGGGGATGGAAAAACACCTGTGGTGATGTTAGCGTGTCTTCACTGGGTGGCAACTATGGGCTCAAGTATTTGTGTACTGCTTGAATAAAAGCATCTGAGTGGTCTTGATGGGGAGGGAGCTGAGACTATGCAGCCAAAGTTTGGGTCCTTTCAAGAGAGGGGTCTAGTGGGTTCATAGGCAGATGGGGAAGCGTCACCTTTCCAGAGTGGTTGCTGTCTCCCTGAGTTGCTGAGATGATGTGCATTTACTGAGAAGGTTTCTAAAGCCTTGGGAGGCTGTCTCAGCCAGCTCAAGGTCCTTAGCAAGGGTGCCTGCTGGCAGCAGCACTGGCACTGACCCGGCCTCTTCCCTGTCTCCTGCTGAGTGCTGGGGAGTGGGGGCCTCTCCGAATTGCCCTGGCAGTGAAACCTGCCCTGCCTAAAAAGAAAGTCTCTAAAGATGGGGGAATTTAGCCAAAGCCACAAAGCGTTGGTTAAGTCAGGATTTAAATGCAGAGCCTGACTGGGGCTTTTTTGTGGTGTGCTAAGGATCTGATGGGGCCTTGTGTATACTAGGCAAAAGCTTTGCCCTGTGCTACAGCAGTCCTGGAGTTTGTTTAGTTTTGTTTAAGACAGGGCATGGCTCTCTAGCCCAAGCTGGTCTTAAAGTGCAATTCTTATGCCTCTGCCTCCTGAATGCTAGGATCCCAGGTGTGTGCCACCATGGCCAGCCACCATAGGTCTTCATTAAGAAGTCGAGCTCAAGCCGGGACTGGTGGCGCATGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCAAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGACTACACAGAGAAACCCTGTCTCAAAAAAAAAAAAAAAAAAGAAGAAGAAGAAGAAGAAGTCAAGCTCAAATGTGTTTGTTAATATCTTACAAATCTGAATGCTCATCTGAACATTAAAATACACTTAGCAATGTAAAGTGAGAACGAGTTTGCAGATGAGCTGGACCCCAAGGGTGATTGGACGCAGACCTGCTGTCATAACTGTCAGCTTAATGTGGCTCACAGACACTGCCCTGTCTGTGTGGACAAGCAGTGTATCTTAAAAGTCTAGTTAACGGGCTGAAGAGATGGCTCAGCAGTTAAGAGCATCAACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGAGATCTGATGCCTTCTTCTGATGTGTCTGAAGACAGCAACAGTGTACTCATATGTATAAAATAAATAAATCTTTAAAAAAAAAAAAGTCTAAAGGTAGAAAAAGTAAGGTTTGAAAGCCCAGAAACTTGTATTGAATGAGTTGCTGCCTGTGAGCAAGGCACTGCTTGGCATTATCAGATACACTACTGCTATATAGAAGATTCTTGAGCAGAGAGAGGTCTTAGCATACACAACGCTCTCTTGGAGCTCGCACCTTTAGGCCATGTTTCCTAACTGGCTTATTGACAAACAGCTTTGCTCTGCAAGAGAATGCTGATAGGGAAATAGTCAGCAATTTGGGCAGAGTCTGTCCCTTCTTTATGCATTGTCCAAAGAAAAGTCATAGAAGAAAATTTGATGTAATCATACTTGCGAGGTATCTGAAAGCCCAGCAGTACCTGAGACATTTTTAGTTGTCAGTTAGGAGAGTGAAGCAGGGACTGCTGGGTATCCAGCAAGTGGGCATGCTGGTGACCATCCTGTAGCAGCAGGGTGTCTTCCCCAAGGCCCTGGATGTTCCTAGTGCTGAAGTGAGACTGCCCTATAGCAGGAGCTGCAGCCACAGCCTGGGAGTTAAAACTCAACCCTGCAAGTCCCAAGGCTCTTGAGTGTGGACTGCTGTTTAGTGCAGGCCCCAGGATGGACCCCGCCATAGCACAGAAATGAGAGGACAGTGTCCAAAAACCATGTGGTGTAGACAAGTTGCTGCTGCCCGTCATCATTTGTCATTTACTGTCTCTGTCACCTCTTACATTTGCATGTGTTTCATGTTATCCCACTTGTGACTTTCCCTGTTAAATATGTGGGGATTTGAAGCACAGGATTTCAGTGCAGACCTAGACCCCTGCTGCTTCCTGGTCTTCTCTTTGTCCAGCCCCCGCGCCTTTGGCTTCACACCTGTTGTCTTATTTGTTCTCTAGCCCTGTGGAGAAACTTTGTCACTTCTATTACACAGTATTGACTGTGACCCACTTGGTCTAATTAAGTCTGTTTTATCCACTCTATTCCACCTGTCTTTCCAGTCTGGCTTTATCTAGACACAGTAGTCTTCTCATAGAAAAAAAAAAAAAAAAGATCAGCTCTTTTACAACCTTTTAGCAAGCCTAGCAGTGAGCTGTGGATTGTTAAAGGTAGCAGAGAGAGTTTAGTCCTGTCCTGAAAGTCCAAAGCTAACCGTCATTATATGAACAGTTAACAGCATCCAGAAGGGCTCAGATTGGGTGAGTTCCCCAGCCTTTGGGCACCTAGATATTGGCTGGATCCTGGGGCTCCACTGTAGACTCCTGGAGGGCTTCCCTGTTAGCTCTCTAGACCTTATGTAAAGCAGACAGAGAGATGCCCCTGCTGCAAAGCCTGGCACAGCTGAGCTCTGTTAGACATGCCTTCTTGCAGAACCACTCGGTACAGAGAAGGAAAGATGTTGAGTTGTCTTTACACAATCTTGGTTCCAGTTTTTTGTGTTTGGCTGTGTTGTGTTGTATTGTATTGTATTGTGTTGTGCTGTTGTAACTTTGGCTGTCTGAAACTTGCTGTGTGAGCAGACTAGTCTGGAACTCACAGAGACATTAAAGGCGTGTAGTCAACACTACCTGGTTCCAGCTTTTTTTTTTTTTTTTTTTTTTTTTTAAAGATTTATTTATTTATTTATTTATTTATTTATTTATTATATGTAAGTACACTGTAGCTGTCTTCAGACGCACCAGAAGAGGGCATCAGATCTCATTACGGGTGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTTCGGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCAACTGAGCCATCTCTCCAGCCCTGGTTCCAGCTTTTTATGTGCTGATTCTAATTGCTCCAGGCCCATGACTTGGCCCATGACCACCTGATTCACTGTCCTGCAGTGCTAGAAATACAATTTAGTTTCCATGAAGCAAAAAGGCCAGGGCTGCCCATAGAGTAGGGATTCTAAAGGTCACACTGGATAGCTGATGCTGCTCTGAAGTGAGGCAGTAGCTGAAGACAGAGGCCATGTTGTGTTCCTTCCTTTTCCTCTATACCTGTCCCATTGCTTAGAGTCCCAGGACAGAGGAGCACAGGTTAGCTTCCCCTCACCTGTATCCCCTTTACTCATTTATTAATTAAGAGCTTTGAACACAGGGCCCTCTAGGACACATGTGTGCCTGTGTGTACACGTGCATGCTTACGTGTGGTGTGGGTATCGTTTGCTGTGTTATCTAGGCAGTCCCAAAGCTCTTGTTATCTCCTGTGTTGCTGGAAGCAGTTGTGTGAGAGCAGGTCTGACCATGTTGCTTAGGCTGATCTCAGACTTGTACACTGCAATTATGAGCATGCCCCACCACACCAGCTTCCCCCGCACTTTGGATCTGCCTTGTCTGTACTGTCCAGGCTGTGGAATGAAGCCTACCAGGTTTGTGTTCTAATTTTGTTACATAGGCAGGCTATCTATTCTACCCACTCCCCATGCAGCCTCAATTTCTCCACTTATGAATTAATAGCATCTGTTCTGTGGGGAGGTTACAACCTGAATGGAAACAAGTGCAGAGCTCTGGGTAGCTTGAAGCACTCAGAGCGGCAGCTATGACTTGGCCCTTTCCTCTGCACGCAGACTTTTGCAGCCTCTGTCATCCTCCTCTGAGTTCTCACTCTGACCCCGATGTAGTGTCTCTTCAGTTATTAGTGGCTCCCTGCCTTGCCCAGTCAGTCTTCTCCTCTGTTGTTGTTTCTATGTTTCTTCCACTGTTTTTTTGGTTTTGGTTGGTGGGGTTTGTTTTGCTGCTGGGGATGGAACCTGTGTCTGTCCTAGGGTAGACAAGTGCTTGGTGAGCTCCAGCTTCAGCCACCCACTTCGACTTCCTTAATAACATAGGGCAGATACAGTCATCTGTCCCACAGACAAGGAATGGCATCTACTGTTTCCAAGTCCAGCTTGGCCTTGGATCTTGACCCTTCCCAGGATTGACAACCTCATAGAGTCCCCAAGCTTATGAGGACACGTGGTAGCAGCTGTTCCCCTAGAGAAGGAGAGGTCTGTAGGTTGACAGTCATTCTGGGGTGACTTTATAGGCCAGCCAAGCAGGTGCTGTGCATGTTATGTGTATAACTGATTCTGACTGCTAACTACAGTCTACAGCCCGAAGGGCTCAGGGAGTGCAGACCTTTAATAAAGAGACCGTCATTAAGGCGTGGGACTTGGGAGACAGTACAGATGCTACCTGACTTTGCCTACTTAGTTAGCCCCTCACTGAGTCCTGCTGGCTTGGCTCTTATGTGCCTGATTTGATCTCTTCTTGTGGCAGGAAAAGCCCTTCTACTCCCAAGTGCCTGCACTTTAAACTGTTCCCAGCTCCTGTTCACTCTTGCCTATGTGTCTGATGTGTTTTCTTAAAATACTTCCTGTTCCTCAGCAAGATCATCATTCTTGCCTTCCTGCAGGTGGTGTTGTGTCAAGACAGCCCCTTCTGTTTCCCCCCTCCTCTCCTCTTTTTCTTTCTCCCCTCCTCCTCTCCTCCTCCTCCTCCTCCTGTAGCCTGACTGCTCTTCATGCTGTCACTAGCGCCACCCCTGTGGCCTGATTATTCAGGCTAGCCCCGCTGTGGGTATGTTAAAACTGAGCACTCTTATCCAGGCAGTAGAGAAACCAGTGCTCAGCCTCTTAGAGACAGACAAGAATTGAGTGTTTCAAATGGAGATGGGAAAACAGCGCAAGGAAGGCTGAGTAGTCCTGGTGGTCTGCAGAACACTCCAGGAAGCCATACCAGGCCTTTGGCAGGTCTCTGGCTGAAGTTCTGTTTACTTGATTCCATCCACATATATAGAGGTTTTGGGGTTGTTTTGTTTTGTTTTGGTGTTCCTATGAAAAACCTCCCATATTGGATTTTAAATTTTTAAAATTATACTCCCTGACATTATCTGGGGGTGGGGAAGATTTAGTATTCAAAAGAATAGTTACTTTTTATAATATTTCTGCCATTCATGTATTTATAGATTATTGCTTAAGTCTCTTGACCTCAGTTGATGTTAGTGACACTCTCTGGACCTTAGGAAGCCCACAGGTAGTGGCCTCGCCTATCCACATATCTCTTCACTCCCTCTGTGGGCTATTTGTGGGACTATCCACTCGAGATGACTGTCAGTGTCTGGGATCTGGGCCACTGGAGAAGGGAGATGGGGAAAGGAGACTAGAGCAGCATGCCCTGCTCCCTGCTAGGTGTGAATCTAGGCTACCCACAGTCAAGGAGGAAAGAGTGGGGTTAGGAGGAGTTCTGGAAAGTTGGGTGCTGGCTTTTTCCTTCAGGTGTCTTTCCTTGGCATCGAGCGACCGAGTGCCGTTAGTAGCCGTAGTACCGGTAGTCAGAGTTACTAGCGTCGGCTTGGTTTCCTGAGCTCCTCCTTCCAGCACTGGCATTGGAGGCCTTGGAAGCCGTGTCTCTAATGGACAGGGACCTACAAGTTTGAATAGGTCTATGTGAGGATCTAGGTGGCGGATGGACTGTGATGCTGCCAGTTCCTCAAATCCTCTGAGAATGTATGTGCCCTGGGGCCTGACTATTGCTCCCCTGTGTCCTCACCGAGACCTCACTGTACGGTGGGAGATGGGAAGTGCTATCTCAGGCAGCCAATCAGAACAGAGGAGAAGGTTTTAAGGATCTCCGAGTGTGGGAAGGGAATCCCCTAGTCTCCAAATGACCCTTCTAGTCCTAAGCCTGTCTTTCTTCCTATTAATCTTTGTCTCCTGATCACAATCCTTAGAGAAACCATCTGGCTTGGTCCCTGCTGCCAAAGCGTTTTCCATTTGCAGGAGTATCGAGCTAGTTTATAGATTTCACTGTTTTCAGAATAGCTCCCTTTAATCTTCTCTCATTCCTTAAACATGGCATTCCCTTTCAG
Seq C2 exon
AACCTGTGCTGGCTGGAGGAGAAAGAGAAGGAGGTTGTCAGTGCCTTGCGCTACTTTAAGACCATTGTGGACAAAATGGCCATTGATAAGAAGGTTCTGGAGATGCTCCCGGGGTCAGCCAGCAAGGTGCTGGAGGCCATCTTACCCCTGGTGCAGACTGACCCTCGGATCCAGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844-Rapgef1:NM_054050:3
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.105 A=NA C2=0.000
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:
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: