DreINT0173554 @ danRer10
Intron Retention
Gene
ENSDARG00000044718 | vav2
Description
vav 2 guanine nucleotide exchange factor [Source:ZFIN;Acc:ZDB-GENE-091204-420]
Coordinates
chr21:18007728-18008031:-
Coord C1 exon
chr21:18007963-18008031
Coord A exon
chr21:18007815-18007962
Coord C2 exon
chr21:18007728-18007814
Length
148 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGA
5' ss Score
5.29
3' ss Seq
TTTGTCTATGTCTTTTGAAGGAC
3' ss Score
9.25
Exon sequences
Seq C1 exon
GAGTTAGTGAGTCACTCTATGGACCGACCAGAGAGGCAGCAGCTTAAAGAAGCACTAGAAGCCATGCAG
Seq A exon
GTGTGAACTCTAATACAGCTACCATATACTGTTTGCTTTTGGTTTGTAATTTAACTGTGCTGAACATATTGCTTAATGTGTAAATATATCTTAGTATTTCAGTAATCAAGTGGTGTTTTAATGAGTGTTTTGTCTATGTCTTTTGAAG
Seq C2 exon
GACCTGGCCATGTATATCAATGAGGTGAAGAGAGACAATGAAACCCTGAAGAAAATAAGTGAATTTCAGAGCTCTATAGAAAATCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044718:ENSDART00000143987:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.043 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062115=RhoGEF=FE(12.6=100)
A:
NA
C2:
PF0062115=RhoGEF=PD(4.0=24.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGAGTCACTCTATGGACCGA
R:
AGAGCTCTGAAATTCACTTATTTTCT
Band lengths:
139-287
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]