DreINT0124553 @ danRer10
Intron Retention
Gene
ENSDARG00000079291 | rapgef3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:ZFIN;Acc:ZDB-GENE-090312-38]
Coordinates
chr23:33490784-33491025:+
Coord C1 exon
chr23:33490784-33490868
Coord A exon
chr23:33490869-33490964
Coord C2 exon
chr23:33490965-33491025
Length
96 bp
Sequences
Splice sites
5' ss Seq
TCTGTGAGT
5' ss Score
7
3' ss Seq
TTTTCACTCTTTTTTTGTAGGTT
3' ss Score
11.24
Exon sequences
Seq C1 exon
CCCAAGCCAGAGAACCCCAGAAGATCTGGAAGTTATTTATGAAGAACTTCTGCACGTCAAAGCTGTGGCCCACTTGTCTACATCT
Seq A exon
GTGAGTCGACACTCACTGAAGCATGTCATATTTGTTTGTGCCACCAATTTTAATTCGGCCCTCATTTGTTCGATATTTTTCACTCTTTTTTTGTAG
Seq C2 exon
GTTCGTAAAGAGCTGGCATCAGTGCTGGTATTTGAAAGCCATGCCAAGGCGGGAACAGTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079291:ENSDART00000142328:4
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(10.3=42.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGCCAGAGAACCCCAGAAG
R:
GACTGTTCCCGCCTTGGC
Band lengths:
143-239
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]