RnoINT0124188 @ rn6
Intron Retention
Gene
ENSRNOG00000014316 | Rapgef1
Description
Rap guanine nucleotide exchange factor 1 [Source:RGD Symbol;Acc:619793]
Coordinates
chr3:8236382-8237113:+
Coord C1 exon
chr3:8236382-8236518
Coord A exon
chr3:8236519-8236999
Coord C2 exon
chr3:8237000-8237113
Length
481 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
CCAGGTTTCCTCTCTTCCAGGAG
3' ss Score
9.2
Exon sequences
Seq C1 exon
ACTCTCAGCGCTCTCATCTCTCCTCCTTCACCATGAAGCTGATGGACAAATTCCACTCTCCTAAAATCAAGAGAACACCATCCAAGAAGGGAAAGCCAGCTGAGGTGTCGAAGACTCCTGAGAAGCCTGTGAGCAAA
Seq A exon
GTAAGCTGCGCCTCTAGGTGTTCCTCCTGGGCCCAACCTGTGGCCAGCGTTGTGGGCTGCACTGTGTATAAGTGCGTTTACTAGAGCCATCTGTGTCCCTGGGACCTGGGACCTTAGGATGGTACGTGCCTGTCCTGCTAATCAGTCCGGCCAGTGGCTTGGACAGTTCCGTGTCATCCTCTGGGCATTTAAAGTAACTCTGAGCACTGTGCTCACACCTGGTGCTACCTCCCACCCAGAAGCCCTCGGGTACTTTCACACAGGGCTCTGATGGCCTGAACCAGTCGTTCAGCCTCAGGGCCTGGGCTCTGAAACTCACAACCCCCTGAATCCCATCTAAAGGCATCCTCCAGCATTAGTAACCTCAGCGAGGGCAGCTGAGCCAGATGTGTGGAACAGCTGTTGATTCTCACCAACCCCTTCTTCCAGTCTACAATGTCCATTTCAAGCTCTGTAGGAATCCAGGTTTCCTCTCTTCCAG
Seq C2 exon
GAGGCAAGAGACAGATTTCTACCAGAGGGCTACCCTATCCCCTTGGATCTGGAGCAGCAGGCAGTAGAATTTATGTCCACCAGTGCTGTGGATTCCAGGTCTCAGAGGCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000014316:ENSRNOT00000060977:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.609 A=NA C2=0.158
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TCAGCGCTCTCATCTCTCCTC
R:
CTTCTGCCTCTGAGACCTGGA
Band lengths:
247-728
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]