HsaINT0179972 @ hg19
Intron Retention
Gene
ENSG00000134215 | VAV3
Description
vav 3 guanine nucleotide exchange factor [Source:HGNC Symbol;Acc:12659]
Coordinates
chr1:108113782-108116820:-
Coord C1 exon
chr1:108116669-108116820
Coord A exon
chr1:108115995-108116668
Coord C2 exon
chr1:108113782-108115994
Length
674 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TGGTTGCTTTTCTTTTTTAGGTG
3' ss Score
12.15
Exon sequences
Seq C1 exon
TGTTAAGTCCAAAAGTGCTGGGCATTGCCATCGCTCGGTATGACTTCTGTGCAAGAGATATGAGAGAGTTGTCCTTGTTGAAAGGAGATGTGGTGAAGATTTACACAAAGATGAGTGCAAATGGCTGGTGGAGAGGAGAAGTAAATGGCAGG
Seq A exon
GTAAGTTGGCCCTCTCGATGTGCTGGTGCATGTGAAAGAAGGGGACTGAGCAGTTGTTTGCACCCATTGTGGCACCAGGGAGAAGCCTCTATACTGTATTACAGCTTTCAGCCCACAGGCCTCTGCCCTCTGGAAACTGGTGCTGTGTTTTGCTGATACCAGGGACTCGCTGAAAATATTTGAAATGAATATGATAGTGACATAAATAAAATTCACCTGGGCAAGTGGGACAGCTTGCTGCTTGGAAAAGAGTCGAGGAGCATTTCAGTTCTTTTTAGACCCTGAGCCATAGAGCTAAACTTTATGTGTATTGCAAAATATCTATAAGAACTGCTGATGTAAATTGGAAAGAATGGGACATAGTACCTCTGTCTTTTCATCCTGTTCTACAGCAGAAATAGGAATCATTATGCAGCAGAGCCCCCCTGTATTATACTTAATTTACATATTTATTTGTGTGCTAGTGGATTAGAACACTGTTTATTTTATTCCTCCATTTCGATCATTTACTCTATTAGGCTTCTAAGAGCAGTTAAACCAATCTTCTCACCTACAATGGACATAAAACCCCAGTTTAATTGGGGTGTTATGAAAACAAAATACTCTGTTTGTAGAATCCTTTGAAGTGTCAGATACAAAGTCATGTTGCTGTGTTGGTTGCTTTTCTTTTTTAG
Seq C2 exon
GTGGGCTGGTTTCCATCCACATATGTGGAAGAGGATGAATAAATTCAAATCCCGTGTTGCACCCTGCACCAAAAATTTCAGAGAAGGGATAAATAGAAGCCTGCACAGCATCGTGAATTAACTGAAGTGTTTAAAAAGCTGCATTTCTGGCTGTTCAACATCCTCCCTCCTTAGCCCCTCCTAAGTCTTAATGCTGAGATTTCTAAAGATGCTGGTACTGACAGATTAATGGCTTGCCTAGAGCTGTGCAAGAAACAGCCTGCCAGTCTGTCATTGTCAGGGACCAGGGCAAAACCAAGAGCTGTTCTTCCCAGAAGAGCCCTGCAAACACATTGGTTCGTGCTTCCCTTTACTTCTTCTGGTCAGATACCATGAATGCCAGTCATCAGTAAATCTTAATACACTTTTGCTTTATTCTCACATGCCATTCACCAGATTATTTGATGGTACAAAGAAGCAGAAGTGTAATTTTCCTTTTCCCAGCATGACGAAAAATTGGAGTTCTGCCATTTGAGCAGCTTACTGGAAAGATCCAGCCTTACTTGTCTTAAATTGTCCAACAAGGTGACTCATTGCCCGGCAAACACTTTTACCCTCAGATGTTACTCATGATATTATAAAATATGAGGCCAGTGCTCAGGTTTGCATCATAAGTGAGCTATCCCTGAAGGGTTTTAATTACTTATTTGGTGTCCTGATTATATTTGCAAACTTCTTTATAAAAGGTGAAAAAAGCACACAAAAGAGAGGGTGTCTTCATATTAAACCTTCACAACCTTCATGATTTCATAGGATTATTTTGGAAATATAGCACTTGACTTTATGAAAGGATCTGGGCTAGGTATATTAAGGGTAGTTGCCAATAACCTGAAGAAGCTGGCATTGTTTACAGAAACAGATCAAGGGCTATAATTTATGTCATTTTATAGCAGCAGTATCTATTAATACATGCCTTTTCCTCCCATCCACCTCCCCCGCACACACACAAAGATGACCTGGGACATGATTTTTTTATTCCCACATTTTCTTGGAGCACAAACAACTTTGTTGAGGATTTTGGAAGGAAAGCACAACTGGGTCCTTTATTCATTTCTGGGACAGAAAGAGGGTCAGTGGACTTTTGTGGGCCTCCAGCTTCTCTCAGAGTCTCCCCCTCTGCAGCCCATCCTGGGAGTGTATTAACTGGAGGGAAGATGGGTCTTGCAGTACATTTGTTTTGCCCAGCCATCACTCTTTTTTGTGAGGAGCCTAAATACATTCTTCCTGGGGTCCAGAGTCCCCATTCAAGGCAGTCAAGTTAAGACACTAACTTGGCCCTTTCCTGATGGAAATATTTCCTCCATAGCAGAAGTTGTGTTCTGACAAGACTGAGAGAGTTACATGTTGGGAAAAAAAAGAAGCATTAACTTAGTAGAACTGAACCAGGAGCATTAAGTTCTGAAATTTTGAATCATCTCTGAAATGAAGCAGGTGTAGCCTGCCCTCTCATCAATCCGTCTGGGTGCCAGAACTCAAGGTTCAGTGGACACATCCCCCTGTTAGAGACCCTCATGGGCTAGGACTTTTCATCTAGGATAGATTCAAGACCTTTACCTCAGAATTATGTAAACTGTGATTGTGTTTTAGAAAAATTATTATTTGCTAAAACCATTTAAGTCTTTGTATATGTGTAAATGATCACAAAAATGTATTTTATAAAATGTTCTGTACAATAAAGTTACACCTCAAAGTGTACTCTTGGAATGGATTCTTTCCTGTAAAGTCTTATCTGCGACTCTGTCTCGGGAATGTTTTGTCTGTTGCCGTCAGCCGAACTTTGTTATGGAGGGAGCAGCCTCACACAAGCAGAAACACTCCTGTGGATGGTATTGTAGCATGTATTGTTTATTTTAGTCAATAGACCCTCTCCTTATAAATGGTGTTTAGTCTTCCTGTTGCATTTCATGGGCCTGGGGGTTTCCTAGCAGAGGATATTGGAGCCCCTTTTTGTGACATTACCAATTACATCTTTGTCCACGTTTAATACTTTGTTTTGGAAAATTTAAATGCTGCAGATTTGTGTAGAGTTCTAATACCAAAGACAGAAGTAAATGTTTTCCATATACTTTGTCTTGCCTGTATGCAGCCCTCGTGTAATACGGTGAATTAGAGTGGTATTTCACTTTGTATTATTTTGTAAATATGTCAATATAATAAATAGTGACTAAATTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000134215-VAV3:NM_006113:26
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0765312=SH3_2=PU(75.9=80.4)
A:
NA
C2:
PF0765312=SH3_2=PD(20.4=78.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGGCTGGTGGAGAGGAGAA
R:
GGCTCTTCTGGGAAGAACAGC
Band lengths:
354-1028
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)