RnoINT0124224 @ rn6
Intron Retention
Gene
ENSRNOG00000059961 | Rapgef3
Description
Rap guanine nucleotide exchange factor 3 [Source:RGD Symbol;Acc:621869]
Coordinates
chr7:139244736-139245230:-
Coord C1 exon
chr7:139245118-139245230
Coord A exon
chr7:139244825-139245117
Coord C2 exon
chr7:139244736-139244824
Length
293 bp
Sequences
Splice sites
5' ss Seq
CCGGTAACA
5' ss Score
5.92
3' ss Seq
ATTGACTGTCTTCCCCCTAGATA
3' ss Score
10.08
Exon sequences
Seq C1 exon
GATGTGGAAGCAAAAACCATGAGACTGGAAGAACACGGCAAAGTGGTGTTAGTTTTGGAGAGAACCTCTCAGGGTGCTGGCCCTTCCCGCCCTCCGACCCCAGGCAGGAACCG
Seq A exon
GTAACAAGCCTATCACATCTCTCCCCACGCAGCTCCACACGCTGCCCTACACACTACCTCTCCCACTTCCAAGCCTTGCTTGGTATCCATGCCATGGTCATGTCCCTTGGCTATCTAGGAGTATGAGGCACTGAGGAGGGACTGAGGGACCGAGAGGATGTATCAGTGCCTCCTCTCCAAGACAGAATAGGGCTGGCCAATCAGAAGGCACGATGTTATCCATTATTGATGTCTGTGTACGGAGGGGTGATGTTCTTAGGGCACATGCTATCGATTGACTGTCTTCCCCCTAG
Seq C2 exon
ATATACGGTAATGTCTGGCACCCCAGAGAAAATCCTAGAACTCCTGTTGGAGGCTATGAGACCGGATTCCAGTGCTCATGACCCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000059961:ENSRNOT00000078644:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.161
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(2.4=5.3)
A:
NA
C2:
PF0061815=RasGEF_N=PU(24.8=90.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAGCAAAAACCATGAGACTGG
R:
CTGTTGGGTCATGAGCACTGG
Band lengths:
197-490
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]