RnoINT0124233 @ rn6
Intron Retention
Gene
ENSRNOG00000059961 | Rapgef3
Description
Rap guanine nucleotide exchange factor 3 [Source:RGD Symbol;Acc:621869]
Coordinates
chr7:139237051-139237433:-
Coord C1 exon
chr7:139237308-139237433
Coord A exon
chr7:139237233-139237307
Coord C2 exon
chr7:139237051-139237232
Length
75 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTG
5' ss Score
4.87
3' ss Seq
CTGGTCTTTACCCTGTCCAGGTG
3' ss Score
8.23
Exon sequences
Seq C1 exon
ACCCCACACCCTGAGCAGCTGGGGCCCACTCTGGGTTCTTCTGAGATGCTGGACCTAGTGAGTGCCAAGGACCTGGCAGGCCAGCTCACAGAGCATGACTGGAACCTCTTCAACAGGATCCACCAG
Seq A exon
GTGCTGGAGGTAGAGCTGAGGGGTGTGGGCAGGACACCGGGCCTGGCATGCTGACCTGGTCTTTACCCTGTCCAG
Seq C2 exon
GTGGAGCTGATCCACTATGTACTGGGCCCCCAGCACCTGCGGGACGTCACCACTGCAAACCTGGAGCGCTTCATGCGACGCTTCAACGAGCTGCAGTACTGGGTGGCCACCGAACTCTGTCTCTGCCCGGTTCCTGGCCCCCGGGCTCAGCTACTCCGGAAGTTCATCAAGCTGGCAGCCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000059961:ENSRNOT00000078644:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.190 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(12.9=57.1)
A:
NA
C2:
PF0061714=RasGEF=FE(32.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACCTAGTGAGTGCCAAGGA
R:
AGTACTGCAGCTCGTTGAAGC
Band lengths:
176-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]