RnoINT0124263 @ rn6
Intron Retention
Gene
ENSRNOG00000001516 | Rapgef4
Description
Rap guanine nucleotide exchange factor 4 [Source:RGD Symbol;Acc:621886]
Coordinates
chr3:58893605-58894190:+
Coord C1 exon
chr3:58893605-58893683
Coord A exon
chr3:58893684-58894043
Coord C2 exon
chr3:58894044-58894190
Length
360 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
GTTGTCAACTGTCTCTGCAGTTT
3' ss Score
7.17
Exon sequences
Seq C1 exon
CACAAGGTGCTTTTGCAGCAGTTTAATACAGGTGACGAGAGGGCCCAGAAGCGTCAGCCGATTCGTGGCTCTGATGAGG
Seq A exon
GTAAGTGATCTCTCTAATTTCTTGTGTGGAATAATTATTGTTGGGCTAAAATCTGCTCCCTGGAAACCATTGCCTTGAACCTACCAAAAAGCTGCTCTCGGGTGTGCTCCTTGGTCCCCTGATAAGTTATGTTCTTGGGATCTGGTAGCCAGACAAGAGCCGAGACGCTTACTCAAACCTCAATGACCCTGCCTGTCCCCGGCTGGCAGCATCTCTTCAAAGGATGTGGGATCTCTTGGGGTTTGGTTGGATGCCCAGCACTAAAGTCCCCACCCCAGCAGAGCTCAGGCCCTGACCACCGATGTCTAAGTACTTTGAATGACCAAGACCACTTTCTCACGTTGTCAACTGTCTCTGCAG
Seq C2 exon
TTTTGTTCAAGGTCTACTGCATTGACCACACCTATACCACCATCCGAGTGCCTGTAGCCGCCTCGGTGAAGGAAGTCATCAGTGCAGTAGCAGACAAACTTGGCTCTGGGGAAGGCCTGATCATTGTCAAGATGAACTCTGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001516:ENSRNOT00000010630:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0078818=RA=PU(2.5=7.4)
A:
NA
C2:
PF0078818=RA=FE(61.2=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:
TTGCAGCAGTTTAATACAGGTGAC
R:
CTCCTCCAGAGTTCATCTTGACA
Band lengths:
214-574
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]