GgaINT0039991 @ galGal4
Intron Retention
Gene
ENSGALG00000001915 | VAV3
Description
guanine nucleotide exchange factor VAV3 [Source:RefSeq peptide;Acc:NP_996745]
Coordinates
chr8:1001300-1003301:-
Coord C1 exon
chr8:1003214-1003301
Coord A exon
chr8:1001430-1003213
Coord C2 exon
chr8:1001300-1001429
Length
1784 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
AGTGTTTTCCTTTCTGCAAGGAA
3' ss Score
5.08
Exon sequences
Seq C1 exon
GTACAATAACGAAGTGAAACATATCAAGATTTTTACAAGAGATGGCTACTTCCACATTACAGAAAACAGAAAATTTATAAATTTAATG
Seq A exon
GTAAGTATTGATTAGGTTTTTAACAATGTGTGATTTCTCTGTAACTTTTGCTGTTGAAGTGTGTGCTACTTTCCTATGTGGAAATGCAGAAGGATGAGAGATTTGAATTACGTCCATACCTGCAAATAAGGTATTTTTTGGTTGTTACGGTTTATGCTTTTAGTCATGGCAACATGTGCTTAAAATTACATACTTATATTTAGGTATGGAATGTATCCCTTACAGTGGTGTAGAAGAGAGGAGGAATTTGAGTCCCACTTTGAGTGCTGCTTGCTTACAAATTTCTGTTTCTGTTGCCTTGGTAATTTGAATGATACGTGAAAGAAAATTTGTTTGCAGACAGTGTAGCTTGCCTGCTGTGCTAATGTCAGATAACAAAGCCCCAAGAGTTCTTAATGTCCTGGCCTTCCTGCTTGCTGTAGTGTCTGGCAGTCTGTGATGATGAACTGTTAAAAGCAGGAGTAGATTTTTCATAGCTTTAGCTTCTACCTTAGGAACAGTCTACAAAAGCTTGCAGCATGTGAAGTGAAGTGCTCCAGAGTTTGCCTCAGAAGATAAGCTTTGGACACTCATCAGAAATGTGATGTATGCATTAGATCTTGGGAGCCATTTTGTTGGCTGGAGTTAATAATGATCACTGAAGGTTTTGGGTTTTTTTTTAATTTTTTAATTTTATTTTTTAACTGGAAGGAAATAATTGAACATGGTTCTATTTCCTTATTTTAACCTTTGCTTGGCATGGTCAACTCTTCATTTTGGGAATCAGGATGTAACTATGTAGAATGGAATGACTGAGTAGTTACTGAAAGGAGGGAAGGATTTAGAGTAAATGCACTACTTTTTGATTGCACTTCAGAAAAGTGAAATCCCACAGTTGAAGTATCATGAATCAAATACGATTGCTTATAATTGTCTAGTAACTTTTAATTTTAGTCCATGCTCTGTGTAAAATCTGTATGATACCGTCACTGTTAGAATGGATTCAAAGCTAAGAGACAGTGACAGCTTGAAGATGTCAAAGGGAAATTATTAGCTGTCAGTATTTGGATCTGTACTGTCTTCTTTAGAATATTAATTTAAGTAATTTATCTCCCTGGTTACTTAAACTATTTGAGCCAGTTTAATGAACTGAGAGAGAATTGCAGAATTTTTTTGGATTGGGCCCAAGCAGTATATGAGCTGCTGTTTTTTTTTATTTAGGGTTCACTCTGAGGAGGAAAAACTAACAGATTTTAATGGCAAAGCCTTGACATTTTTACATGGTCCATTTATCTGCTCAGTCATATGTCCGTTTTTTATGTGTAATCCTTATATGCTTAGTTGAGATCTGTGTGCTTATAAATTCATTAGTCGATGAACATTACTTATTGTAGAAGAAATTTGAGAAAACAAAGGCAGTTATCACTACATGCTTAGTGAACAGCTAACCTTGCTTTTATGCCTGACTTCAGAAAAGCAAATAGGTGCTTAGCTTTGTTCAACAAAGCAGTAAGTGTTGACTCCAACTATACAGCTGTGTTTGTTTTTAAAGTCATATGTATCATTTTTATGAAAAATTAAGTTTCATTTTAAAAATATGTTCTGTACTTCAGGGTAAGGGTTAACTAACGCAGTTAAGTTGCAATATAAAAGCAATCAATATTTATTAGGCTACTTGATTTCTTAATGTACGTGTTTTGTGGGATCATAGCAGTTTATTTTATAAAACTGTCATTGACTGTTCACCAGAATCATGAAAAGGATGTGATTTCAATTTCCGATGACAGTGTTTTCCTTTCTGCAAG
Seq C2 exon
GAACTTGTAGATTACTATAAGCACCACTCTCTCAAAGAAGGCTTTCGAAGTCTGGATACTACACTTCAATTTCCGTACAAAGAATCTGAAAACTCGGTGGGACAGAGGGGAAACAGAGCAGGTGGCAACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001915:ENSGALT00000002946:23
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=0.106
Domain overlap (PFAM):
C1:
PF0063014=Filamin=PD(2.9=33.3),PF0001719=SH2=FE(38.7=100)
A:
NA
C2:
PF0001719=SH2=PD(6.7=11.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTTTACAAGAGATGGCTACTTCCA
R:
AGTTGCCACCTGCTCTGTTTC
Band lengths:
190-1974
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]