MmuINT0131757 @ mm9
Intron Retention
Gene
ENSMUSG00000049044 | Rapgef4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:MGI Symbol;Acc:MGI:1917723]
Coordinates
chr2:72016235-72018160:+
Coord C1 exon
chr2:72016235-72016356
Coord A exon
chr2:72016357-72017976
Coord C2 exon
chr2:72017977-72018160
Length
1620 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
TGCCTCCATGTTTCCCGCAGTGG
3' ss Score
9.02
Exon sequences
Seq C1 exon
ACAATGCTGTGTTGGGACTGAGCTGGTAGACTGGATGATACAGCAGACATCCTGTGTTCACTCGCGGACTCAAGCTGTTGGCATGTGGCAAGTCTTGCTGGAAGATGGTGTCCTCAACCATG
Seq A exon
GTAAGATGAGCCACAGGCTCTGGAAAATTCTCAAGAAATGCAAAGCGTATTTCTCTGGGTAAGCTATTGCTGAATTTCCAAATGAGCAAGAAAGAATTACGATCCCCTTAAAGAACCACCAAGCTAGCATCTTCATTTAGTAATACAAATGCAGCGAGCGGATGCTATTGATTGCAATGTTCCACATTGAACCTTCCTAACTTCCGAGAATGAAGGAAAGGAAAATGAAATTGCAACCGGAGTGCATCAGCTCCAATTATGTTTATTAGTTTGCATTCATGGTTCATTGATAGTGTGATTATACTCCAAGCATTGCATAGCGGTCCTGATGCAGGGGCAGAGTGAGAGAGCAATGAAATGTGTGGCCGGGCTGATGACATGAGAGTCAGTAATGAATTCAGACACTGCCTTTTAGCTGTGCCACTGTCTGGGAGAGCCAATTTGTATACCGGCAGGATGACCATATTTAAAATCAGAGCTGCGCTCTGCAATTGCTGTCTCCAGTCACTACCGCGGCTCTCGCTGAACAGAAGAGCTAGCCGGGGGCTGGCGGGCGCCTGTCACTGAACTGCTAATGCCACTTGTTTAAGACTACTTTTCTAAACATGAAAATATTCAAATCATCCATTTCACTCGCCGACACCTGGGAACGTGGGAATAATAATTTTGCTTGAGTTTCTCAGACTTTAATGTGCATTCCAATCACCTGGAGCTCTTGCTGAGATGCAGATTCCAACTTTGCAGTCTGGGATGGATTCTAAGCATATCGGTTTGCAAGAAGTACCCATATGTGGCTGTTGCCCCTGCAGCTGCCCTTGCTGCCACCGCTGCTCCCATCCCTGTTTTGGGGACCTAGAAGGGTCTACCAGTGTTCTCTGTCTTTTGAACATATTGACAACCCAAGCTATAAAGGGACTAAATGACGTTCAGACACTTAGACAAGAGATGCTACCCTAGTCTACCCTTTTTTTTCTAACAGAGATCTATTAGATCTTGTTGTTGATCACTTCGTTAATATCTGTGAGTTCCTGGGTTTAAGTCCCCAGCTTTGCCAAAAGAAAGGGAGGAGCATTTCTCTGCAAGAAAATGACCCCAATTTCCTTCAAGAGTCTGTGATCTAGAAGCATGGTCTAGTTGGCTGTGTTCATATCACTAATTAATACTCTTGTAGCCATCCTCCCAAGTGGGATGAGAAGTATGCCTAGCTGCATATAGAAAGAATAGCATAAGTTCTGACTTCCCAAAGGAATGTCTCCTGTAAGACTGTCCTCTCAAACAAGCATTCTCAGACAGGAGCTGACCAGTTTGGGACACATGCCCTACCCTGTAGAAAAGGCTACCCCAAGGCATAGTGTGCAAGTTCCATAAAAGCTGGCAGGTGCTCAGCAGGAGGCCCAGAAAGTCCAAAGTCGGGTGGTTCTAAGTGGCTGTGGCAGAAATGACTGCAGTTGGCATGGCGTCACTGCCGGCTGCCCCGCCTGGGTGAGGTGGAGTTTGAAGGACTCTGACTCTGCTGTTAGCTGCACAACTCTTGTCAGACTCCTGCCCTGTATTCCTGGCAGGGAACTGTGGGATGCGGCTTCAAGCCCCAGCTGACCCTTGCCTCCATGTTTCCCGCAG
Seq C2 exon
TGGACCAGGAGCGCCATTTCCAAGACAAATATTTATTTTATCGATTTCTGGATGACGAGCGTGAGGATGCCCCTTTGCCTACTGAGGAAGAGAAGAAGGAGTGTGATGAAGAACTTCAGGACACCATGCTGCTGCTCTCACAGATGGGCCCTGACGCCCACATGAGAATGATCCTGCGAAAACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049044-Rapgef4:NM_019688:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.210
Domain overlap (PFAM):
C1:
PF0061016=DEP=FE(57.7=100)
A:
NA
C2:
PF0061016=DEP=PD(21.1=24.2)
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:
ACAATGCTGTGTTGGGACTGA
R:
TTCGCAGGATCATTCTCATGTGG
Band lengths:
302-1922
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: