MmuINT0131765 @ mm10
Intron Retention
Gene
ENSMUSG00000041992 | Rapgef5
Description
Rap guanine nucleotide exchange factor (GEF) 5 [Source:MGI Symbol;Acc:MGI:2444365]
Coordinates
chr12:117714105-117715404:+
Coord C1 exon
chr12:117714105-117714249
Coord A exon
chr12:117714250-117715306
Coord C2 exon
chr12:117715307-117715404
Length
1057 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGC
5' ss Score
6.3
3' ss Seq
CGTCTCCATCCTCTCCGCAGACC
3' ss Score
12.37
Exon sequences
Seq C1 exon
CTATTCTGCCAAGAAGTATCAAGGGGAAGAAGAAAACTCAGATGTCCCTTGTCGGAAGCGCAAGGTCTTACATCTGGTTTCCCAGTGGATTTCTCTGTACAAGGACTGGCTACATGAAGATGAGCATTCAAAAATGTTTCTAAAG
Seq A exon
GTGTGCCAATGCTTTCAGATATTTTGACATGATTGATTTTATTTTCAACTCTGTGCTTCAAAAATCTCATTTTTGGTCATTCAATTTTTGTGTCCAATTCAGTGAAAATATAAATTCATCTTGACTTCCAATGCCTGGCATTCTCTATATAAGTCGGAACTCAATTTTTAAAAATTTAAATATATTATGAAAAACTATGCATGGAAGTTTTATATGCACCAATTTTGGGTGGGTTGTTTAAATCATCAGAATTTTTATTGTGAGTTAAATAACATAATGCCAAAATATACTTTAAAATTTGATGCTACTTAATGTTAGATATATGATAATGTTAAAATGACAATGTCTATACAGGCAAATAAAACTTAGATATGTATATTGTATTATTATGTGAATTTTAACTATATCCTATGCTTGAGAATTATATTTGAGAATAGGCTTTTGACAATATACTTTGAGAACAGTAGCAATCTGAAAGACACTAACCTAGATAAAGCAGTTTGTCTAAATATTGATAGTTTACCTGGAATAGAGCTTGACATTGTGTGCACAAGTCAGCACATAGAGAGGATAGACTGGGATTTTAGCAAGACCATAGAGGAAATGGCATTGAACTTAACATTCCTTTTAGGCTTCCAGTTAAAAGCTTATCTCACTGTCCCTCTGCCTTAACTCATGTTATTTCTTAAGCCCACTGGTTATTTTAATATATTTTCCTTCCAAGCAGTCATGCAGATACTCTCTTTTGAGATCTGAACTACTCGTGGATGTCTGTAGTAGCCAACTAAGAGATGTCTGTTTTCAGCATCTGCTACAGTCTTTAAAAGCAACCAGGTTGTTGAGTGGCTGGAGACCACATTACTTCCTGGAATAAGAGAGCCATTACCTGAGACTTTTTCTTCATTGGCGGTGTTGGGATTGAACTCAGGGACTTAACACAAACTAAACGTGTGTTTGACCACTGAGCTGTATGGCCAACCCTGTCTTCATTGAAATCCTCACCGAACACACGCTGAAGTGTTATGTTTGCCGTTTGTCGTCTCCATCCTCTCCGCAG
Seq C2 exon
ACCATATACAGGAACGTGCTGGATGATGTCTATGAGTACCCGATTCTTGAGAAAGAGCTGAAAGAGTTTCAGAAGATACTTGGCGTGTACCGCCGTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041992:ENSMUST00000109691:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(43.6=100)
A:
NA
C2:
PF0061815=RasGEF_N=PD(5.5=18.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGCCAAGAAGTATCAAGGGGA
R:
CGGTACACGCCAAGTATCTTCT
Band lengths:
233-1290
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