RnoINT0124226 @ rn6
Intron Retention
Gene
ENSRNOG00000059961 | Rapgef3
Description
Rap guanine nucleotide exchange factor 3 [Source:RGD Symbol;Acc:621869]
Coordinates
chr7:139244051-139244480:-
Coord C1 exon
chr7:139244402-139244480
Coord A exon
chr7:139244211-139244401
Coord C2 exon
chr7:139244051-139244210
Length
191 bp
Sequences
Splice sites
5' ss Seq
CCAATATCC
5' ss Score
-12.74
3' ss Seq
TTCCCTTGACTGGTGTCCACCTT
3' ss Score
-5.41
Exon sequences
Seq C1 exon
AGACATTCCTCAGTGACTTCCTGCTGACGCACAGTGTCTTCATGCCCTGCACACAGCTCTTTGCCGCCCTCCTGCACCA
Seq A exon
ATATCCTTCCAGCCCCGGGATGCTGTGGGTAGGGCATGGGATGGTGTGTTGCGTGTGGAGGTGCGGGAAGTAATCCCTATCGAAGTGGCTGCCGTGACCCTTCCCTGGCACCCGGAGCATGCCTGACCCAGTCGGGCCCTGCACAGCGGGTGCTTGGACGGCATGTTGTGGTTCCCTTGACTGGTGTCCAC
Seq C2 exon
CTTCCACGTGGAGCCATCAGAGCCTGCCGGGGGCAGCGAGCAGGAACGCAGCACCTACATCTGCAACAAGAGGCAGCAGATTCTGCGTCTGGTCAGCCGGTGGGTGGCCCTCTACAGCCCCATGCTCCGCTCAGATCCCGTGGCCACCAGCTTCCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000059961:ENSRNOT00000078644:12
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=0.235
Domain overlap (PFAM):
C1:
PF0061815=RasGEF_N=FE(23.0=100)
A:
NA
C2:
PF0061815=RasGEF_N=FE(46.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCCTCAGTGACTTCCTGCTGA
R:
CTGGAGGAAGCTGGTGGCC
Band lengths:
234-425
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]