HsaINT0179899 @ hg19
Intron Retention
Gene
ENSG00000141968 | VAV1
Description
vav 1 guanine nucleotide exchange factor [Source:HGNC Symbol;Acc:12657]
Coordinates
chr19:6828430-6828719:+
Coord C1 exon
chr19:6828430-6828498
Coord A exon
chr19:6828499-6828632
Coord C2 exon
chr19:6828633-6828719
Length
134 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CACCCCTGCCCCCTCCCCAGGAC
3' ss Score
9.88
Exon sequences
Seq C1 exon
GAGCTGGTGAAACACACGCAGGAGGCGATGGAGAAGGAGAACCTGCGGCTGGCCCTGGATGCCATGAGG
Seq A exon
GTGAGTGGGTGTAGGGTGCTGGTGACTCACCTGCTGCAGACACCCTCCTGGTAGGGGCTGATCCTCTAGCCGGGATTAGGTAGGAGCCTGGGTCGGCTGTTGGGGGGCCAGGTTCACCCCTGCCCCCTCCCCAG
Seq C2 exon
GACCTGGCTCAGTGCGTGAACGAGGTCAAGCGAGACAACGAGACACTGCGACAGATCACCAATTTCCAGCTGTCCATTGAGAACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000141968-VAV1:NM_005428:11
Average complexity
IR-S
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:
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
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAACACACGCAGGAGGC
R:
GGTTCTCAATGGACAGCTGGA
Band lengths:
147-281
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)