MmuINT0131735 @ mm9
Intron Retention
Gene
ENSMUSG00000049044 | Rapgef4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:MGI Symbol;Acc:MGI:1917723]
Coordinates
chr2:72039105-72043800:+
Coord C1 exon
chr2:72039105-72039220
Coord A exon
chr2:72039221-72043711
Coord C2 exon
chr2:72043712-72043800
Length
4491 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
TTTTTTTTCTTCTTGTCCAGGTA
3' ss Score
11.37
Exon sequences
Seq C1 exon
GACGTTGAGGCGAATACAGTCAGACTTAAAGAACATGACCAAGATGTCTTGGTACTGGAGAAGGTCCCAGCAGGGAACAGAGCTGCTAATCAAGGAAACTCACAGCCTCAGCAAAA
Seq A exon
GTATGTTTGCATCCAACACTGTAATTGCCAGACTATGATTAACCTTTTCACATGGCATCGTTTCTACAATAGCATGTTCTCCTTTTTGTGGAAGACGGAGTGTGGGTGACTTTTTTTCTCTCTCTCTATTGACTAATCACACATCTTGTGGCGTATAATGTATCCATTTCTGGCACTACATGGAGCTTGGTGCTGGGTAGAGACATACTCTGAGAGTATTGTCCTGCTCCAAAGCCTCTCCCTCTATACTGTTCAGCCTTAACAGCCTCAAAGAGAAGATCCCCAAGAGAACAATGCCAGGCAGTGCAGGGCGCAGGCCCCAGTGATGAGACGCTGTGGTATTTGAATGCCCTGGGGAAGTTTCAGATAAAGTGTTTTCCCTTTGCTCTCAGAGTGACTGAGGACACGGATGAGACCCTGATTTTGAGTAGAAAACATGTCGTCGCATTGAACTCCTGGCCACCCATTCTTGCCAGTGTCAAATGGAAGTCTCACTTCACATTTCTGGAGCTTCCTGTTTGTTTAACTGGGGTCGTTTCCGGAGCACCCGGGCTCCGTTTCAGCGTTTGCTGTAACTCCCTTCCTAAGACTGTTGCACAAAATGTACCAACATTTGTGTGGTGAGACAAGAGACTTAGCAGTGAGCCTCTAGGAGATCGGGGCTTGCTGTTTTTTTAAGTGGGGATTCATTTCCAATCTGTGTATAAGAAAAGCAGATGAATGTTTGTTTACTAAGGAAACATCACCAAATAATATGTTGAGGGAGCATTTCCCTTTGTTGGCAAGTACAGTGGGGTTCCCTTTATCAGCGCGCTCACCCAAACTGATGAGTTCCTATTGTTTCCACTAAAAGCCTATGACTCCGATGTTTTCATCTGGGTAAGTCAACATATTTGAGAAGAAGACAGGAAGAAACATATTATTAAATAAGCACTGTATGCTTTGTAGATTGTCTCTAATCCTTACAACAACCCTGTTTAAGGGATGGAGGCATTTCGCTTGCTCAAGGACTCCTTAAACCCATGACTCTCAACCTTCCTAACACTGTAGCCCTTCAGTACAGTTCCGCATGTTGTGGTGACCTCCAACTGTAAAATTATTTTTGTTGCTACTTCATAACTATAATATTGCTACTGTCATGAATCTGAATGTAAATATCTGATATCTGACCCCTCTGAAGGAGCTGACAACCCACATTCCCCCACCCTGAAGAGGTTATGACTCATAGGTTGAGAACCACTACCTTAAAGGGAAGTTCAACTTGGCCGCCTTCCACACCTCTGGTCCCCATTCTTCCTAGATTCTCTTATCAAACGAGAGTAGTGTGCTGCATGGGTGACAAAATACGCAGAGTGGGGGCTTGCATCAGGACATATCCATCTGTCTCACGCCCGTGGGAATTCCTTACACAATACAGAATGGCTACTATTTATGTCACAGTTACTATCAGTAAATATGAGGTGCTATCTGTAAGTCTTCAGTTCGAGGTGCCTTCCCCTTTATGAATTCAGTGGAATGAAAACTCAAACCAAAGGTGATAGAAGAGACTGTGTGTCTGACTTTTATTTTAATACTGTACCGGTTTTCTACTGGTGTCCTGCCATCCGGTCCAAATTTCTTACATAATTTAAAGATAATGCACGTGTGAACATTTGTAGCAAGCTATTTGTATCGTGCACTGGGTACAAAAGAATACACCACAAAGTCATCTTCCAAAAGAACGCAAAGCTTCTCTCTCCTAAGAGGTTACTTCCCCAGACTGACTGGAAATAAAAGGAGAGCCTGGGAGTAAATTTTATGGCTGATGTTCTCATCAACCTTAACAACATATCAACAACCGTGTCTGCAGACACACAGTTGAGGGTATCTGTCTCTGTGGAAGTTGTTCTTTTTAAACTCAGAGAACATCATCACATTGGTGGCAATAATGTTATTTTTCTGATTTATGCCCCGCCCCATCCCGAGAAACCTAGGTTAGTTTATGTATACACTTGAAGCTTGAAAAACTGCCTGACTCTGCCCAAGCCACTGAACAGTGGATGCTTCATGGATGCTGATATTAAGTCAGTGGTCTGGATGATGCAGTTACCATGATACCCACTTTGGGGGATGTCTTGGTCCCTGGGTTGTGAGAATTCAGTAATTTGAGACGATTGTCCTGTTCATGTTGGGGCCATGCCCTTTTCTTTAGACTAGTTTTCCTGCTCAACAGTCCCCAGCTTGTTCACAGGAAGAGCAGCAAAAAAGTTCCTCCACCCCTGGCCCTTGCTTTGGTTGTTCTAAATGCAGACTTGGTATTAGGGAAAAAATTTTCTCTCACAAGTTTAAAACAACCTGCTGACTGATACAATGTAGCCAACTGGGGTGAGTTTTTGATCAGAACGGGAGTAGCTTCTGCTTGCCATAAACTGACAAAGGTTGTGCCATCTGGTCTCAATCGCTCTTAACCCCTATAGAGCAAGGGCTCAGGTCGTAGACACCTGCCTGTTTCTGGTATGATGTAAAGCCAGAATCTGGTGTTTTGGGCAAAACTGGGGCCATCCAGAGGTTTCTAAGCCCTCTTTTCCTCTTCAGTCCCCTGCCCCCACTCCTGAGTTCTGTGGCAAATATAGGCTGGGTAAGGAAAGCACAGAGCTGAACCACTAGAGGGCGTCAGGGACCAAAGAAAGATCTTGTGGGGTGTGACTGGCCAGCCAGGCAAAGCCTGAAAGAAGACACTTGCTCTCTGTTGAGGTGACAGCTTGTGTGGCTTGCCCGTGGGTCTTTTGTCTACGTGATCAGGCGGAACACCCTACCTAAGGGAAGTCCAAACAAGGAGAGCCAGAGAATAAACAAAGTGCTTCAGAATGGAAGTTCTGACAATCCGACGCGTAGCCCGTGGATCTCGCTATCCAGACAACACGTGAAGTAACAGGCTCATTCAGGGGTCAGTTAAGGAGTGCATTTATACCCTTATTCAAATAAAAACTGCTTTCGAAAGCCTCCTTGAAGAGGAAGACTTTTAATTACACAGTGAATTTCCTGTTCAAAATGGGCTGTTGACAGCCAGACCTGGTCCCTTCTACACATAGAGCATCTTGCTGCATAGGCAAACAAAAACAAACATCAAACAAACAAAAATCAGCCGCACAGTCGCATTCTCTAGTGTTTGCCAGTTTCTCCACCTGCAGTGTAGAGGTGGTATTAACTAGCAGGAGCAAGTAAACAAGGAGCCTCATTCCGCACCCACCTCATTGTTGGGGACATAGTAAACACCAGAAAGGTGTAGAATACTCTCCCCACTCCGCTTCCCGATTTATCTGGCCATACGCTCCTCCTCATGTAGAGAGTCCTGTTCATATATTCGAGCTGTGCCTCCGTAGGAGAGCACTTGCCTAGCGCTCATACGGCCCGGAGTTCAACCTCCAGGGCTGCCACACTTGCTCTGTCCCCATGTCCTCAGGATCGTCTGCTATCACTTCTCGTCCATCCCTCAGGCAGGAGGTAAGACCCGCTGATGCTGATGAGGGGCTCTTGCCATCTCTATGCACCTCCTCCACAGCCTCGAGCAGGCAAGAAAGGCACAGAGGTGAAGGGGCTAAGGAAGCTGGGTTTGCTCCGAGCTCCATCCTGTCTCTGCTTCCTGAACACGAGAGAATGCTCTTTGCATTGTTATATTCCCTTCCCATCATCCCGCCAAGCAGGAAGGCAGGGTCTGGGTGCTACTGGGGATACCTACACGATCTTCATGTGTTCTGCCCATCTACAGCAAGCGCTTACACTGTCTGCATTCCGACTTTAACTCACGTTCAATCTCAAAATCAACTTGCTCTTGTTGATTGGAGGGTTGGAGGGCACCCCGAATAGATCCCTCAAAATAATGACTAACGCAGCCCCCTAAAATAATTCGTAATTGATATTGAGTAATTTGCATCCAGGTTTCTGCTTCTGATCTAATTCCTGTCCGTGATGCCCCCCGGGTTTGTTTGCTCACTGGTACTTGGGCCTTTTGGTTTCCTTTGCTTTATTATTATTAGAGGATTTCCAAAGCGCGTAGCAGTGCGGAGGTGGAAAGGAGGAGCGTTCCAGAAATCAGCATGAAAATCCAGTGTGACACTGACATTTCTGTGTCCACTGTCCTGTCCTCCCTCGCTCCCCTCCCTGCCCTGTGCTGCCTCAGGTTCATCTCCCTGACTTGTCTCAGTCGCAGCTATGGGAGCTGCTTTCTCAGCTGCATCTTTAGTTCTAGGTAGGGGGAGGGCGGAGAACATTTCTAGTAACTGCATCTACTGACTGTTTTTCTACAGCCTTCTTGTGTGCTTAGGCGAGGTACGTGGTCTTCCTCACTACAGGGAAGTTACTAGTCACAAGTAGTCCGTATGTTTGCCCAGGATCTTGTTTTTCAAAAAATATCTACATCGGTAATTTGTTTCTCCTAATGCATTACTCGCTTTTGTAAGAAACTAATGGTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTCTTGTCCAG
Seq C2 exon
GTATACTGTGATGTCAGGAACACCTGAAAAGATTTTAGAGCATTTTCTAGAAACAATACGCCTTGAGCCATCGTTGAATGAAGCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049044-Rapgef4:NM_019688:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.161
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(2.3=5.1)
A:
NA
C2:
PF0061815=RasGEF_N=PU(26.2=90.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: