MmuINT0131742 @ mm10
Intron Retention
Gene
ENSMUSG00000049044 | Rapgef4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:MGI Symbol;Acc:MGI:1917723]
Coordinates
chr2:72225999-72226621:+
Coord C1 exon
chr2:72225999-72226077
Coord A exon
chr2:72226078-72226474
Coord C2 exon
chr2:72226475-72226621
Length
397 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGC
5' ss Score
7.75
3' ss Seq
ATTGTCAACTGTCTCTGCAGTTT
3' ss Score
7.53
Exon sequences
Seq C1 exon
CACAAGGTGCTTTTGCAACAGTTCAACACAGGTGACGAGAGGGCCCAGAAGCGTCAGCCTATTCGTGGCTCTGATGAGG
Seq A exon
GTGAGCAATCTCTCCAATCTCTCCCGTGGAATATTTCTGGTTGGGCTAAAAATCTGCCCCCTGGAAACCATTGCCTTGAACCTATCAAAGCATTGTTCTTGGGTGTGCTCCTTGGTCCCCTGGTAAGTTATGTTCTTGAGGTCTGGTATCCAGACAGAGCTGAGATGCTTGCCCAAACCTCAATGGCACTGCCTCACCCCGACTGTCAGCATCTCTTGAAAGGATGTGGGATCTCCTAGGGCTTGGTTGGATGCCCAGCACCCAGTCCTCTTCCCACCCCAGAAGAGCAGTGAGTCTGCTCAGGCGGTGACCACAGATGTCTTAAGTACTATGCCTGGCTTATGTTATTCTTTGAATGGCCAAGACCACTTTCTCACATTGTCAACTGTCTCTGCAG
Seq C2 exon
TTTTGTTCAAGGTCTACTGCATCGACCACACCTATACTACCATTCGTGTGCCGGTAGCTGCCTCGGTGAAGGAAGTCATCAGTGCAGTAGCTGACAAACTGGGCTCAGGGGAAGGCCTGATCATCGTCAAGATGAACTCTGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000049044:ENSMUST00000090826:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.130 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0078818=RA=PU(2.5=7.4)
A:
NA
C2:
PF0078818=RA=PD(92.7=76.0)
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:
TTGCAACAGTTCAACACAGGTG
R:
CTCCTCCAGAGTTCATCTTGACG
Band lengths:
214-611
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