RnoINT0124236 @ rn6
Intron Retention
Gene
ENSRNOG00000059961 | Rapgef3
Description
Rap guanine nucleotide exchange factor 3 [Source:RGD Symbol;Acc:621869]
Coordinates
chr7:139236539-139236784:-
Coord C1 exon
chr7:139236694-139236784
Coord A exon
chr7:139236590-139236693
Coord C2 exon
chr7:139236539-139236589
Length
104 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
CACCTGTCTCACCTTCACAGCGT
3' ss Score
9.49
Exon sequences
Seq C1 exon
CCTCAAGGAGCAGAAGAATCTCAACTCTTTCTTTGCGGTCATGTTTGGCCTCAGCAACTCGGCCATCAGCCGCCTGGCCCACACCTGGGAG
Seq A exon
GTAAGTGGCCCGGATCTGCCAAGGCCAGTCCTCTGACCTCCTGGGGGATGTTAGCATGGCTCTCTCTTCCCAGCCATGGCCCCTCACCTGTCTCACCTTCACAG
Seq C2 exon
CGTCTGCCCCATAAAGTACGGAAGCTGTACTCGGCCCTGGAAAGGTTGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000059961:ENSRNOT00000078644:21
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:
PF0061714=RasGEF=FE(16.1=100)
A:
NA
C2:
PF0061714=RasGEF=FE(8.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCAAGGAGCAGAAGAATCTCA
R:
CAACCTTTCCAGGGCCGAGTA
Band lengths:
139-243
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]