DreINT0124556 @ danRer10
Intron Retention
Gene
ENSDARG00000079291 | rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:ZFIN;Acc:ZDB-GENE-090312-38]
Coordinates
chr23:33494013-33494330:+
Coord C1 exon
chr23:33494013-33494159
Coord A exon
chr23:33494160-33494235
Coord C2 exon
chr23:33494236-33494330
Length
76 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TAACCTGGATTTAACTGCAGGAC
3' ss Score
6.39
Exon sequences
Seq C1 exon
GGCTTGGTGACTACGCTTCATGAAGGAGATGATTTTGGCCAGTTGGCATTGGTGAATGACGCTCCTCGAGCCGCCACCATCATTTTAAGAGAGGACAATTGCCACTTTCTGCGGGTGGACAAGCAGGATTTTATACGCATTCTTAAG
Seq A exon
GTAGGTTTGTGTTTGGATAGCTCAGCATGAATTTGAATGTGAGTCCATGGTGTCTTTAACCTGGATTTAACTGCAG
Seq C2 exon
GACGTCGAGGCAAACACCGTCCGTCTGGAGGAGCATGGTAAAGTCGTTCTGGTTCTTGAGAAGAGCTCGGCGCAGGATACACCAAGCTGCAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079291:ENSDART00000142328:7
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=0.094
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=FE(55.2=100)
A:
NA
C2:
PF0002724=cNMP_binding=PD(2.3=6.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGGTGAATGACGCTCCTCG
R:
GCCGAGCTCTTCTCAAGAACC
Band lengths:
171-247
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]