MmuINT0131742 @ mm9
Intron Retention
Gene
ENSMUSG00000049044 | Rapgef4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:MGI Symbol;Acc:MGI:1917723]
Coordinates
chr2:72064056-72064678:+
Coord C1 exon
chr2:72064056-72064134
Coord A exon
chr2:72064135-72064531
Coord C2 exon
chr2:72064532-72064678
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-Rapgef4:NM_019688:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0078818=RA=PU(2.5=7.4)
A:
NA
C2:
PF0078818=RA=FE(61.2=100)
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:
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
Other AS DBs: