RnoINT0124190 @ rn6
Intron Retention
Gene
ENSRNOG00000014316 | Rapgef1
Description
Rap guanine nucleotide exchange factor 1 [Source:RGD Symbol;Acc:619793]
Coordinates
chr3:8300842-8301158:+
Coord C1 exon
chr3:8300842-8300926
Coord A exon
chr3:8300927-8301063
Coord C2 exon
chr3:8301064-8301158
Length
137 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGA
5' ss Score
8.55
3' ss Seq
ACTATTCTGTTTCCACACAGATT
3' ss Score
9.51
Exon sequences
Seq C1 exon
GCCAGGAACCTTGCATGATTTCCACAGCCACGAGATAGCTGAACAGCTGACACTGCTGGATGCCGAGCTTTTCTATAAGATAGAG
Seq A exon
GTATGACTGAGTGGCCCTGCAAGGAAGGCAGCTAGCTCTCTGCCTGGAAGCTATTGATGGCTGTCCCTATGGAGAGCCCCACACCCAGACCCAGGAGCACCAGAGACTACAGCGCTGACTATTCTGTTTCCACACAG
Seq C2 exon
ATTCCCGAAGTTTTGCTTTGGGCCAAAGAGCAGAATGAAGAGAAGAGCCCCAATCTGACCCAGTTCACAGAGCACTTCAACAACATGTCCTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000014316:ENSRNOT00000060977:21
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=0.094
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(12.9=79.3)
A:
NA
C2:
PF0061714=RasGEF=FE(17.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGGAACCTTGCATGATTT
R:
AGTAGGACATGTTGTTGAAGTGCT
Band lengths:
179-316
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]