RnoINT0124193 @ rn6
Intron Retention
Gene
ENSRNOG00000014316 | Rapgef1
Description
Rap guanine nucleotide exchange factor 1 [Source:RGD Symbol;Acc:619793]
Coordinates
chr3:8302606-8303290:+
Coord C1 exon
chr3:8302606-8302707
Coord A exon
chr3:8302708-8303192
Coord C2 exon
chr3:8303193-8303290
Length
485 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
AACCCATCCGTCTCCTGCAGGGC
3' ss Score
9.81
Exon sequences
Seq C1 exon
CACCTGCGCAAGCTCAACAATTTCAACTCCTACCTGGCCATCCTCTCCGCACTGGACTCGGCCCCCATCCGCAGACTGGAGTGGCAGCGACAGACCTCAGAG
Seq A exon
GTGGGCGCTGGGAAGTAGCCTGGGCAGGCTGGGCAGGGCCTGAGCAAGACAAGGCAGGGGTCCCCATCTGGCCACTCATCTCTCATGTGACTGGGACTGCTGCCTGCCCAGCGTCAGACCCTGGTGCCTGCTCTCTCCAGCCAGCAGGTCCAGGGACTTTCATGGTTGGTTGTGGGGTTGTCACCTGTCTCTGTCCCTGGGCCTCAGGGTCACCTGTAGAGTCTACTCTTTAACCCATTCATCCAAAGTGGGCTCTGGGCTCAGCACTGCATTGGGCTGCTGCGTGGGTTTCAGCATAGTGAGGGCAAGATGACGGACAAGTGAGCTCCGAGAAGGGCATGTGCTCTTGCCACCCACAGAGCATGTCACACAGGCCCGAGGCCCTCTGCCAGAGTTTAGCTGACACCATTAACAGCAGTCCACAGGGCCTGAGTCTGGCATGTTGTGGCATCAGCACCTATCACTAACCCATCCGTCTCCTGCAG
Seq C2 exon
GGCCTGGCTGAGTACTGCACGTTGATTGACAGCTCATCCTCCTTCCGAGCCTACCGGGCTGCCCTCTCAGAGGTGGAACCTCCATGTATCCCATACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000014316:ENSRNOT00000060977:24
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(18.5=100)
A:
NA
C2:
PF0061714=RasGEF=FE(18.0=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:
CGCAAGCTCAACAATTTCAACT
R:
GGTATGGGATACATGGAGGTTCC
Band lengths:
193-678
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]