MmuINT0131675 @ mm9
Intron Retention
Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29544627-29554605:+
Coord C1 exon
chr2:29544627-29544783
Coord A exon
chr2:29544784-29554516
Coord C2 exon
chr2:29554517-29554605
Length
9733 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CTCCCCCTTCTCCCTCACAGGAG
3' ss Score
11.17
Exon sequences
Seq C1 exon
CTCAGCCCTCTCCTCCTGTTATAGCCGAGTATACCAGAGCCTCGCCAACCTTATCCGATGGTCTGACCAGGTGATGCTAGAGGGCGTGAACTCAGAAGATAAGGAGATGGTGACAACTGTGAAGGGCGTTATCAAAGCTGTCCTGGACGGAGTGAAG
Seq A exon
GTAAGAAGTGCAGGTCCCAGGCAGCCCAGATCAGGCAGCCAGCCGACAGAAGCTTAAAACTTGATTTTAGACCATACACAGGGTGACTGTCTTCCAAAAGCTGTGATATGGGCCAGCTCTAGTTCTGTCCAGTCACTACTTCACTCTAGAGACCACCAGCCCTTCATGCATCTGGCATTAAGTCCTCTATGGGCCATATGTCCCAGGTATGGCAGAGAACATGTGCCAGCTTAATGCAATGGAGATGGTTTAGCAAGAGCCCCAGTCTATCACCCATCTCCTTTGCATGGTCTGCAAACATGTAGGACTCCTGGTAGAAAGCACGGTGGAGTTGCTGAAGCTAAGTGTGCTTGATCTCTGTGATGTGGTCAATGTGTTTACTATCCAGGCCATTGCAGAAAGCCTCAGAGAAGATAAGGAGCCACAGTTGGAGGGGGAAGCAAAGACTACAAAGGGCCTGGAGTGGGGCCCAGAAGCAGGCTAACTAAGAGTGTCAGTTCCAGTAGGGGAGAAGCAAAGCTGAGTGGGGGCCCGAGAGATGACAAGGGCCTTGCAGTGGCAGCAGCAGGAGGCACTGTTCTAAGAGCCCTTATTAGGCTGGTGGAATGCTTTAAATCCCAATTCATCACTAAGTAGTCTGTGGGCTCAGACAGTTACTACCTTGGTTCATCTTGATGATGCCCATGCACATGCTCAGAAGCACGGGTAACAGCAGGGCCCTGCATGGCAGCATTGCAGACTTAGTGCAGGATGCTTTAGAGCAATGCTGAATACACGTAGCCCAAAGGCATTCATGGCTGTTCAGTATTATGTGGTGCTAAATGCATGCTTGATAGATGCGGCTTGGAAAAGCTGTGTCCCTTTTATTTACCCTCAATCCAAAATTATAACCACACTTGTCAGCCTAGGTCAGAAAAACTTCCATTCTCAGCCAATCTATGAAGTTCCTGAAACATGCCTCTTGGTGTAGTGTTTTTTAGAAGCTCTTAAAAACAGAGCTTTTAGGGTTTTAATTACAGAGAGAAGGCCAAGGAGGCATTGCTTGGTGAGAGAAATCACTCCCAAATGGGCTGTTAGCGAAAGCCCCAGCACCTTTAAAGTAGAGGCTGTGTGCTGCTGTGTCTCCAGAGAGCTTTGGGTTCACTGTGAGGAGGAGATGTGGCAACACTGCTCCCATGCTGTCTTCTCACAGAGCCATCAGACTTTATACCATCAGTGTTAAGAGGCTGCAATCTCTGTAGAATTTGGGGTGCAGTTTATCCCCTCAGTTCTTCCTGCAGCTTCTCTAGCTGGGCAATGTGAGACAGGACCTTCCCAGGTTTTCTGGCCAAGTTCTGACTCTCCCACTCTTGCTGCTCTTGTACCGACTTCTGGAAATCAAAATTATTTTCCAGACCAGATTGTTAGTGTTTCTTCTATCAAATTGATCTTGATGAAATATTATAAGTTAAAACAGCTGAAACAAGAGGTCAGGTTTCCACAGAAGCCTCAGGACTCCAGAGCCCCCATGTTCCTTATGGACTCCTGAAGGCAGGGCTGCACTGGTTGGCAGAAGGAAGGCTTGAATGAAAAATTGATGATTTCTCAATGTGACCCTGGGATGGGAGCACACACGTACAGCCTGTAGAAGTTGAACATGCCAGCACCTGAGAGCAAATAACTTCTTCACAGGTGTTTTTTTTAAAAATAGTTTAGGCAGAACAGGGTAAGGAGAAGGCTCAGCAATGTGGAAGGCAGAGCCAGGAGAGTCCTGAGGAGAAATAACAGAGACTGTGCCTTGGAGAAAACACACTCTGAAAAGTTGTCCCCTGCCCTACACACACATGACCATGCAGGTGAGCAGACACATGCACAAGCACACTAGCACACATACGGATGCTTCCGTGGGTAAGGAGCTCTGTATTCTGGGGGTGCTATGACAGGAGTACTCACAGAGGTGAAGACAGGGGCACAGGTCTGGCCTTGGGGAGCTTCAGGTTACATAAAAGGATGCCACGTGCCAATGCAGGGACAGGAAGTCAGCTGGCATGTGTTACTAGAGGCTTCTTCTAGAGGGTGTCAGTCAAGGAGTGAGATTGGTCAGCGTGGGCATTTGTGATTAGTATCTTAGAGCAATAATAGCAAACAATTCACGGGTGCTTTTCTACACTGCCCAACTTTACTTGTAACAGCCCTAACTGAGGCAGACACCTTCTCTGATGGGCCAACCGAGGTTCAGTGGCAAGCTCATGATTCTCACACATGCCTGCTAGGCCTACGCACTTAGTCACCCTCTGCTGCCCCATCCTAGGAGACCCAAAGGATCCTTCTCATTCACACTTCCTAACAAGGACACCTCAGAAGCCTGTGTCCTGGTGTGTGCTCCAGCCGCCCTCAGCTGGGAGAGCCAGAGTGTGCAAGCACAGTGCTTTAGCTGTTGTCTTCTTCCCACTTGGAGGTACATTCCTTCAGAGTGACTCACCGCCCCTCAGGGAGCTCATTCAGTTGTTAAATGGAATTGTTTGGGGTGGGGTTGGGGGTAAGACTGAAAACTTGTCTGAAAGGCAGATGATTTTGGTATTGTTCCTACATGGAAACTGTCATCTGCCGTGTAAATCTTCACGTAAATGCCACTTGTGAGCTGTATAAACGTGGACAAGTGACTCCTCTGAGATTCTTGTAAGTTCTTAAATACCCAGAGTGTGTTAGGAGAGGTAAGATTGTGTCTTTGGAGTACTGGCAAGGGTTGGGTGGCTAACAGGCAGGATGAGCACTGGTCACCTTGGCAACTTTCACCAGAGTAGCTTACATTTACGTCTCAGGGGAGAATTGTATTTCCCTCTAGGGCAACTCACAAGTTTTGGGTCTTCTGTACTGTGCCAGTTAAATGCCCACTTCTCCTCTGACCTCAGACATGTCAGGAGCAGGCCTCCAGCCACTCAGACAGACTAAAGTGTTATCATTTAAAATAATAATATGGGCTAGAGGCTAAGAAAATACTCCCTGCTCTCCTGGAGGATCCATGTTCTGTTCTCTAGCATCTGTATTAGGTGGCACACAGAGAACTCCATTTCTTGACCTCCATGGGCATCTGGACACTCACACAGACACACAGAAAAAAAAAAAAAACAAAAAAAAAACTTGTAATGCTTTCTTCCACTGAAAGCCTTGGGGAATCCCACAGCTTTGTCACTTGACCGTCACCTCCAGAGCTGTGCTTGCATAGCAGGCTCAGAGGTTTTCTAAGTATAGCAGCCAGGCCAGAAAACAGAAGCTTTTTTTTGTTTGTTTTTTTGTTTTTCGAGACAGGGTTTCTCAGTGTAGCCTTGGCTGTCCTGGAACTCACTTTGTAGACCAGACTAGCCTCGAACTCAGAAATCTGCCTGCCTCTGCCTCCTGAGTGCTGGGATTAAAGGTGTGCGCCATCATGCCCGCCCGGCTAAGCAGAAGCTTTTAACGATACAACTTTTGCAGCTGGTAAAATGGCTGAGCATCGAAGAGTGCTTGCCTCCAAACCTAACCTGATCTGACTGACCCTCAGAACCCAGCGCCCCTAGACGCAGACTGTCCTGTGACCTCCACGAGGGACTGTGGCACACACAATCAACCCATCAATTATTGCAAACATTTTTAGACATAAAACTTTTGGAGGTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGATTTCGAGGCCAGCCTGGTCTACACAGTGAGTTCCAGGACAACCAGGGCTACACAGAGAAACCCTGTCTCAAAAAAAACAAAAACAAAACAAAACAAAAAAATCTTTTGGAGGGATTGGGAGATGGCACAATCGTAAAGTGCTTGCCGCATAAACATGTAGACCTGAGCTTAGATCCCAAGCACCCATGATAAAAAACATAAATAGATTTATAAATTACTAGCCATAGCCACATTAGCCAGGACCCAGTGGCCTCCATATGTGACACAAAAATAAAGTATTCTTTCCCACATGTAAAGAAAGTTCAGTGATAGACAAAGGCGAGTGTGAGGTTTCCTTGAGGACACTTCTAACTCCCTCTTCTACTGTCTGTAACACAGATTCTATGCAGTGATGCACAGTAGCTGCTTCCTCTCCAGTTACCATGGCTACATTCAGACAAGGAAGAAGAGGTGCAAAGTTACCTTCTCCTTTGAAGGAGGCTTCTTAGAGCCCGACACAGAATTTCTCTTGCATTTTATTGGCCAGAGTTGCATCAGGGCTCACCAGTTCACCCCACGTCCACGCATGGCCAGTGCAATATCCTCTCCTCGTTCACTGGCTCCCCAGATTGCAGGGTGCAAACCCTAAGTGACACCTCCTTCCTGAAACCTCCACATGTCACGCTTGTCCTGGAAGGGCAGGGACAAGTGTTCCAAGCCTTGTCAGGCACACATCCTTTGGCACATTCCTTGTTTGGTGCTCTTATTATTTGAGCCAGCCCTACCTTGAGACTGTTCTAGAAACAAGTCCCTGGCTGGTTTTGGCCTTCAGAATGTGGTTTACTATGTTTTTAAAATATTTATATATGTATGTATTTTATATTTATAGGAGTACACTGTAGCTGTCTTCACGCACACCAGAAGAGGGCATCAGATCCCATTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGGCCTCTTAACCACTAAGCCATCTTTCCAGCCTATGGTTTACTATTTTTAAAAGGTTTACTTTTAAAAATCCAGGGCCCAGATAGAGCCAGTGGGTAGCATCGTCTCTGTGGGCAGCAGCTGGTGGGTGCCTCCTCAGCCTCCTCCTCCTCCTCCTTGAAACTTTAGGGCTTTGGTTATTTAAAGTTGTATTCGTATTTATGTGGGCAGTACCCACAGAAGCCAGAATAGTTATCAGATCCCCTGGTGTCAGAGTTAACAGGCAAGTTGTAAGCTGCCCTGCGTGGGTGCTGGGAACCAAACCTACATCCTCTACAAGACCAACCGGTGCTCTTAACTACTGAGTATCTCAGTTTGTTCATTTGAAGCTTTTAAAATTTATTTTAGAGTTATTACTCCTGAAAGTTGGCAGTGTAGAATTAGTCAAAGGCACCCTCATGATGCTACTTAGTGTGTCCCTCTGCCCCTTGGATTCCTGTGAAGCTGGAGGCCAGAGCCCTCTCAGTTTGTTGGTGGAGAAAAGAAGCTTCTAGATTGCACTGTGCTTCCAAGAAAGGTGCCCTCTTGATGTGGGCACTATTGTTGGTCATGACTGCTGTGCCCCAGAGTTTTCAGACTATGACATGTAAGAAGATTTCTTCTGCCAGTTTTCCATCAATAGCCAGAGTGAATCTGAAAGAGAAACTTCCTCTTGTAGCTGTTATACAAAGCTTGTCACTTTCTTATGTATACTTTTCAAAATTAGGAGTGCTTCCTAGCATCCTCTGCCCTGTGTTTCTAGTTTTAAATTGTTATGTAGCTCAGGCCAGGCAGTGGTGGCACACGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACACAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCAAAAAACAAGTTATGCAGTTTCCTAGCTTGCTCTGCTTCCCAGCCATTGTGGCTACAGTATAGCACCTGAAGTCCTGTGTCTTAGGACTGTGTGAGGAATGCCAATTGTTACCTGTCTCCATCTGTGGGTCAAGTCCAGTGCTGCTCGGCTGTATGTGCCACTGAGAGCATCCCTCCACTTGCCACTTCTCACTGCCACTTTAGATGTGGGCAGAGAAAGTCCCTTGTTGTCTCCATTAGAAGTCACTGTGGTGGCAGAGGCAGGAGGATCTGAGTTGGAGGGCAGCCTGGTGGACATAGAAAGGTCTAGGATAGCCAGAACTACATAGAGAGACCTTGTCTCAAAAAACACAAAGCAAAACAACAAAGTCTCTCTGGGGCTGGACACTCCTGTGACCATGTCCTATAGCTCCTGTCACGGGAATCCACCCTAGTCTCCAAGGGCCATTGTGTTCCTCACTTGTCAGACTAGACCTGACCCTCTTCCTAAATGTGTGAAGAACTAAAGGGTGGCACTGAGCCGTGATGTGTAACTGCAAACTTCCTGTGCCCTGGCACTGCACCCAGAGAATAGGGTAAGGAGGTGATAGCCAGGGTCTGGGCTGCAGCTAGGATACTCCCAGTGGAGTGACCCCACTGTGTGAACTCAGGGAACACTATTCACCATGCTGTCCTTGGGGTTCTTTTTTTTTTTTAAGATTTATTTATTTTATTATATGTAAGTACACTGTGTCTTTAGACACTCCAGAAGAGGGGGTCAGATCTCATTACAGATGGTAGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCAGGGCCTTCTGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCAGTCTGTCCAGCCCATCCTTGGGGTTCTTTGTGCCAGGACTGTCACAGCAGTGCGGGGCCCCTCTGCCAGGCAGGTCTTTGTATCATTCCAGGAGAAAGTAGAAAGGAAGCCGGGACCAAGACATTCAAATTCGGAGCCGTGTGTTGACAGAGGTTCCCATTCTCGGGAAAGTCTCCTCCAGATGTGCTCTGTGGCTTAATTAACTGTATGTTGGTCTTCTGTATAGTTGTTGGCAGAAGAGTCCAGAACTCTTTTCTAACTGCCTTGTAACGTGAGACTAACAATTAACTTAAAAGACTGTCTTTGAGAAACCCTGCCTTTCAGAGATTTGGCTTTTCACAAGGTACTGGGCCCTGGCTTACTCACAGGTGGTGAGCACTCAGTGAGACCAGGCTATTGGAAGTACCTAGCTAGAAGAGGTTTCTGGAGCCTTGTGTGTGATCGTTAAGACAAGTTGAGACCAAAGCCCTTCTGTTTGGGCAGGAAGGTTGGCAGAGAAAGAAAAGCTGCCATCCCCTCTCCCAGCTCCACTGTCATGATGTGGTCCTGGAATGTCAGGGCACAATTGCAAGTGTGTGCTTGTCATCCCAGGATCCTATAGCTGTCCATTGTTCATTAGCTGAGGTCACAGCTGCCATTCCAGGACAGCATCCCTGCCTGCTCCCACGTCAGGAGGAACTGGAATTTGTGCTGTGTCAGCAGATACAAATGTGCAGACTTCTCTGCATTCCCTTATCCTGCTTGCTGGAGTACGATTGGCTTAACGTGGAGGCACTCATGATGCTGAGGCAGAAAGATTGAGAATTGAAGGCTTCTGAGTCACTTGGGTCTGACACTTTGATCCCAGCCAAGGCTTTCAAGGGACCTGCCTTTGCCACTCCTGTGCACTCCTCCAGGTAGCGAGTGTGGGAGCGGCTGCCTCCAGCTGCTTCCCTTGCCTCCCTCTGACACTTGTGCTCTGGACTGTGAAGCAAGTCGAAGGCCCCTTCCTGGGGCTAGCCTCAGCCTCCCCAGGATCTTACTTCCACATGACTCCAAGAGCAGAACGGGGTGAGCCTGGATCTGGTTCCATGGACATCCCTCTCATGACTTGGGGGTGGCAGTTTTCTTAGAATTAATTTGTGTCCATTTTCAAAAATGTAGAAGATACAATTAAATACATAAATTACATTAAAAACACACACACACACACAAAAGGGGTTTTGATCTTGTTTCCAAAATTTACAGTGTACCCCATCAAAGCAGGTAGGGCTTTTCTGCACCTAGTATGCCTGGTATTCCACCATCTTTCCATGATGTTACTATGGCCTGTGTTCCTGCTGTGACTTTATTCTTACTGACTTCAGAGTGGCCCTTTGATGGATCTGTCACATCTGCATACTTGGTACTCAAAGTGTTTAATGGTGCTATGAACAGTCTCATTTTACCTGTGGTGACATCCTCACAACTGAGCTTTTACATATATCCATGGCATTTTCCTCAGACAGAATCCTCCTAACAGATACTTAAGGCTTTTGATGCATGCCTGCTGCCCAGAGTGACACTCATTCTTACTGATCCTGTCCTGCCCCACCCTACCGCGTGTCTGCAAGTTTTATTTTGTTGCCATCAAACTTGAGAAGCTCTCATGATCATAACACCCTTTGCATCTGCAAAACTCCTCGTTAATATTTCTTTGTGTATGTTTATCTTTTTTCGTAGTTTTTATGTTGTCAAAAGAAGCTGCTTTGGGAAATGCTAGTTCTTTGCCCCTGGTCAGGGAGATGTGGTTAGGTTACCCAGCTCTGCATTCTCAGAGGTACTGTGTGCTCTTCCCTCGTGCACACAGACCATCACCAGCAGCAGAGAGCAGTGAGGAGATTGTGTGCAGCAATATACCAGAACACTGGTCAGCAGTGAAAAAGAGCCTACCTGGACTCCCTGAGGCAGGTGGGGATGGCCAGAAAGAGAGTGGTCTTTGCCATGGGCAGCCAGAGAGTCGGGGGACTGTGCAGGTTCAGAATTTCTGTCCTAAAGTTGGTTGTGTTAAGGACCGCACATGTGCTCACTCACACTTAGAGTAGCTGAATTTCATGGTATGTGAATTCTACCTCTACAATTTTGAAAGGTGAAGCTGGAGTGATGGCTCATTCTGTAAAGCACATCTCACATAATCATGACCAGAGTTCGATTCCTACAATGCACAGAGAAAGCCAGGTATCGTGGCCATAATTGTAATCCCAGCACTAGGGAATCAAGAGACAGATGGATAGATCCCTAGAGCACTCTGGCCAGTTAGCCTCACTCAGTGTACTCAGTGATCTCCAGGTGCTAGTAAGAGACTCTGTCCCAAAAAAGAAAGTGAGGGCTCCCAAGGCCAACCTCTGATCTCCACCTGTCATGTGAGCATACAGCTATAAGTGTCGCACACACAGGAGGTCCATTTCTATGGCATCCATGGGACAGCCACCATAATGCACAGCCCTTCAAGTGTACACACTGCAAGGCCCATGTATGGCCATCCTGGGGGCCCACAGCAATCTAGGCAGAAAGTACAGAGTGCTGGGATAGCAGAAGGGAAGAACAGGTGAGGGTGGGCTTCCCACCCCAAGTGGTGTTCACACTGTGGAGCATAGCGTTCACCTGGGAAAAATCATTAAAGTGGTCTGGAGTGGTAGTGCATGCCTTTAACCTCAGCACTTCTACACAGAGAGACCCTGTTGAAAAAAAAAAAAAAAAAAAAAAAAAGTCATGGAACAGGATAAAATGTGTCCCAGCTGAAACACCACACCCCTTATCTTCCCTCTTCTCTACTATTTTCAGAGTACCATTTTTTATTTTCTTTCAAAGCCATTTCTCTGCTTTTAGAAGGTCACATAACCTTCACTCTAAGTCCATTGACAAGGCTCCCAGCCAGCCAGTCCACTGGGGCTCCAGTTCCTGCATTGACTAAGCCAGTGCACTTTGGGAAAACACTAAAAGCCAGAAGCCAAGTGGCTAAGTGCACCATTGTGCATAACATGACAGCTTTAAGGAGCCAAAACCGCCTGCCACCCTCCCCAGACTGCACAGGAATACAAGTCTGTAATGGTCTGTTCATCTAAACACCCGGACTTGCCATTTCCCCTTTCAAAAGGAAGTACATGATGCAGTTGAAACTTTGCAGTATGCTGCTATGGTATTTTTAGAGTGAAAGAGGCATGTTAGGGGTTGTGCAGATTACCCCGCGTAGGAAATGTGTGGACACAAATGTGGGTCTTAGAAGCCCTGCCTCTTGCTAAAGGTACAGTGGTGTCATCCCCTCCCCCTTCTCCCTCACAG
Seq C2 exon
GAGCTAGTGAGGCTAACCATTGAGAAGCAGGGGCGGCCATCGCCAACAAGCCCAGTGAAGCCCAGTTCCCCAGCCAGCAAGCCTGATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844-Rapgef1:NM_054050:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.829
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: