DreINT0017698 @ danRer10
Intron Retention
Gene
ENSDARG00000075924 | RAPGEF4 (1 of 2)
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:HGNC Symbol;Acc:HGNC:16626]
Coordinates
chr6:6745263-6745500:+
Coord C1 exon
chr6:6745263-6745347
Coord A exon
chr6:6745348-6745439
Coord C2 exon
chr6:6745440-6745500
Length
92 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGA
5' ss Score
4.8
3' ss Seq
GATGGTGCTGCCCTCTGCAGGTG
3' ss Score
9.88
Exon sequences
Seq C1 exon
GCCTGGTCAAAGAACAGCTGAAGACCTGGAGATTATTTATGATGAGCTGCTGCATATCAAAGCTGTCTCTCACCTGTCCAACACT
Seq A exon
GTAAGAGCATCCCTCCAGAGTCATTTACACAAGTAATGCCCCGTGCTGTTTGAACATGTTAAAATGATCTGTGATGGTGCTGCCCTCTGCAG
Seq C2 exon
GTGAAGAGAGAGCTCGCCGGTGTCCTCATCTTTGAGTCACACGCCAAAGCAGGCACTGTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075924:ENSDART00000166607:10
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:
NO
A:
NA
C2:
PF0002724=cNMP_binding=PU(22.5=42.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTGGTCAAAGAACAGCTGA
R:
AGACAGTGCCTGCTTTGG
Band lengths:
146-238
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]