HsaINT0179914 @ hg19
Intron Retention
Gene
ENSG00000141968 | VAV1
Description
vav 1 guanine nucleotide exchange factor [Source:HGNC Symbol;Acc:12657]
Coordinates
chr19:6852976-6854109:+
Coord C1 exon
chr19:6852976-6853090
Coord A exon
chr19:6853091-6853957
Coord C2 exon
chr19:6853958-6854109
Length
867 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CTTCTGTTCTCTCTCCACAGTGG
3' ss Score
12.17
Exon sequences
Seq C1 exon
GAGCTGGTGGAGTTTTACCAGCAGAACTCTCTAAAGGATTGCTTCAAGTCTCTGGACACCACCTTGCAGTTCCCCTTCAAGGAGCCTGAAAAGAGAACCATCAGCAGGCCAGCAG
Seq A exon
GTAGGAGGTCTCAGACTGGGGGCTTACAGCCTCAGCCCCTTCCCATTGTGGAGGGAAACTTTGGGGATGCCATTGACACCCCTTCCAATGGCCTTGCAGAGGTCATATCTGTGCAGTAGCAGGAACCCCTTTCCACTCCTGTCTATCCCTTCCTATATATATTTTAATATAATATAATTTAATTAATTAATTTATTTATTTTTTGAGACAGAGTCTCACTCTGTTGCCTAAGCTGGAGTGCAGTGGTGCGATCTTAGCTCCCTGCAACCTTTGCCTCCCACCTCTTGGGTTCGAGGGATTCTCATGCCTCAGCCTCAAAATAAAAAAATAAAAATAAAAATTCCAAACCAGTCTTATTTTCTGGCTGGGTGCGGTGGCTCATGCCTGTAACTCCAGCACTTCGGGAGGCCAAGGTGGGTGGATCACTTGAGGTTAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACTCCATCTCTACTAAAAAAAAAAAACATAAAAATCAGCCGGGCATGGTGGCACAGGCCTGTAATCCCCGTGATTCAGGAGGCTGAGGCAGGAGAATCACTTGAACCCAGGAGGCATAGGTTGCAGTGAGCTGAGATTGTGCCACCGCACTCCAGTCTGGGTGACAGAGAGAGACTTTATCTCAAAAAAAAAAAAAAGTGTTATTTTCTAAATTCAGACGGGAGGATGATGCTGGGAGTACAATTGTGTCCCCTTACAGTACAGGGCATCTAATACTCTGCAGAAAAGAGCACTGAGGAGCCCTTTATCCTGGAGTTACTGTCCTGAGAGCTTGTGCCCCCAGAGAGTGAGTGGGTATCTGCCCCAGACCCTTTTCTCACTTCTGTTCTCTCTCCACAG
Seq C2 exon
TGGGAAGCACAAAGTATTTTGGCACAGCCAAAGCCCGCTATGACTTCTGCGCCCGAGACCGATCAGAGCTGTCGCTCAAGGAGGGTGACATCATCAAGATCCTTAACAAGAAGGGACAGCAAGGCTGGTGGCGAGGGGAGATCTATGGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000141968-VAV1:NM_005428:25
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:
PF0001719=SH2=PD(6.7=12.8)
A:
NA
C2:
PF0001823=SH3_1=PU(85.1=78.4)
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:
GAGCTGGTGGAGTTTTACCA
R:
CATAGATCTCCCCTCGCCACC
Band lengths:
262-1129
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)