RnoINT0124247 @ rn6
Intron Retention
Gene
ENSRNOG00000059961 | Rapgef3
Description
Rap guanine nucleotide exchange factor 3 [Source:RGD Symbol;Acc:621869]
Coordinates
chr7:139245571-139245967:-
Coord C1 exon
chr7:139245891-139245967
Coord A exon
chr7:139245718-139245890
Coord C2 exon
chr7:139245571-139245717
Length
173 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TGATTGAGTCCTGGCTTCAGGGG
3' ss Score
2.89
Exon sequences
Seq C1 exon
TGTTCAGCCAGGGGGACAAGGGTACCTCATGGTACATTATCTGGAAGGGATCTGTCAATGTGGTGACCCATGGCAAG
Seq A exon
GTAAGCCCTCCCTCCAGCCCACCAGGGTAGATGTCAACGCTCTTTGCTTCGTGACTTCATGGACACTCCTTTGGATAGTAGCCCCAAGGCTGCTGACCCCACACATATGTCTGAGACTGTCCCTCCCACGGGCTGGTGGGTAGGGGCAGGCTGTGATTGAGTCCTGGCTTCAG
Seq C2 exon
GGGCTGGTGACCACGTTGCACGAGGGAGATGACTTTGGACAGCTGGCTCTGGTGAACGACGCACCTCGAGCAGCCACCATCATCCTTCGAGAAAATAACTGTCACTTTCTGCGTGTGGACAAGCAGGACTTCAACCGCATCATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000059961:ENSRNOT00000078644:8
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:
PF0002724=cNMP_binding=FE(29.4=100)
A:
NA
C2:
PF0002724=cNMP_binding=FE(56.5=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:
TGTTCAGCCAGGGGGACAAG
R:
GATGCGGTTGAAGTCCTGCTT
Band lengths:
218-391
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]