DreINT0124576 @ danRer10
Intron Retention
Gene
ENSDARG00000079872 | rapgef4
Description
Rap guanine nucleotide exchange factor (GEF) 4 [Source:ZFIN;Acc:ZDB-GENE-070912-385]
Coordinates
chr9:2948016-2948251:-
Coord C1 exon
chr9:2948201-2948251
Coord A exon
chr9:2948104-2948200
Coord C2 exon
chr9:2948016-2948103
Length
97 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
TGTTGTCTTTCTCTTTTCAGGAT
3' ss Score
13.92
Exon sequences
Seq C1 exon
AAGCTGCCCAGCAAATTCAAGAAGTTTTATGGAGAGTTTGAAAACCTAATG
Seq A exon
GTAAGTTGATCATAGCGATATTATTGACCAGAGCCGGCCATGACAAATTTGGTCAAACACGGTGTACTCAAAAGATCTGTTGTCTTTCTCTTTTCAG
Seq C2 exon
GATCCCTCCAGAAATCACAGAGCATATCGACTTACAATGGCCAAGCTAGAACCCCCCATCATCCCCTTCATGCCCTTATTAATTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079872:ENSDART00000144046:25
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:
PF0061714=RasGEF=FE(8.6=100)
A:
NA
C2:
PF0061714=RasGEF=FE(15.7=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:
CTGCCCAGCAAATTCAAGAAGT
R:
TTTAATTAATAAGGGCATGAAGGGGA
Band lengths:
135-232
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]