DreINT0124545 @ danRer10
Intron Retention
Gene
ENSDARG00000079291 | rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:ZFIN;Acc:ZDB-GENE-090312-38]
Coordinates
chr23:33510058-33510472:+
Coord C1 exon
chr23:33510058-33510148
Coord A exon
chr23:33510149-33510421
Coord C2 exon
chr23:33510422-33510472
Length
273 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
ATTTTGATCTCATTGAACAGAGA
3' ss Score
5.77
Exon sequences
Seq C1 exon
TTTGAAAGAGCAGAAGAACCTCAACTCTTTTTTCGCAGTAATGTTTGGCCTCAGCAACAGTGCAGTGCAGAGGCTCAATAAAACATGGGAG
Seq A exon
GTAAGGACGAATGCGCTTTCTTAGGCTATATAATAATCTGCCTTTAATAATCTACACTACTCCATTTACATTTATTCATTTAGCAGACACGTTTTTCCAAGGCGCCTTACAAATTAGGACATTCCCCAGTTTTAATGTGCTAAATGTTATAAGTAATACTATAAAGATTACCATCATACTTTTCTTTTCTGAAACAGCTTGAATTGAAAAAAGTGCAATGCTAATTCATTTGACTTAATAAAAAAATACATATATTTTGATCTCATTGAACAG
Seq C2 exon
AGACTTCCCAATAAAACCAAAAGGATCTACTGTGCATACGAAAGACTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079291:ENSDART00000142328:19
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(16.1=100)
A:
NA
C2:
PF0061714=RasGEF=FE(8.6=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:
TGAAAGAGCAGAAGAACCTCAACT
R:
CATCAGTCTTTCGTATGCACAGT
Band lengths:
140-413
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]