HsaEX0032368 @ hg19
Exon Skipping
Gene
ENSG00000091409 | ITGA6
Description
integrin, alpha 6 [Source:HGNC Symbol;Acc:6142]
Coordinates
chr2:173335702-173338993:+
Coord C1 exon
chr2:173335702-173335833
Coord A exon
chr2:173337502-173337618
Coord C2 exon
chr2:173338783-173338993
Length
117 bp
Sequences
Splice sites
3' ss Seq
CGTCCCGTGCATGCGTACAGGCC
3' ss Score
4.92
5' ss Seq
TAGGTTTGT
5' ss Score
4.07
Exon sequences
Seq C1 exon
GGATTGTTCGTGTAGAGCAAAAGAATAACACTTTTTTTGACATGAACATCTTTGAAGATGGGCCTTATGAAGTTGGTGGAGAGACTGAGCATGATGAAAGTCTCGTTCCTGTTCCTGCTAACAGTTACTTAG
Seq A exon
GCCTGCTGTTTTTGACCAGCGTTTCCTATACAGATCCTGATCAGTTTGTTTATAAAACACGGCCTCCCCGGGAGCAGCCTGACACATTCCCTGATGTGATGATGAATAGCTACCTAG
Seq C2 exon
GTTTTTCTTTGGACTCAGGGAAAGGTATTGTTTCTAAAGATGAGATCACTTTTGTATCTGGTGCTCCCAGAGCCAATCACAGTGGAGCCGTGGTTTTGCTGAAGAGAGACATGAAGTCTGCACATCTCCTCCCTGAGCACATATTCGATGGAGAAGGTCTGGCCTCTTCATTTGGCTATGATGTGGCGGTGGTGGACCTCAACAAGGATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091409-'5-9,'5-8,6-9
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=0.263 C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
PF0183918=FG-GAP=PU(43.3=18.3)
Other Inclusion Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTCTCGTTCCTGTTCCTGCT
R:
CCATCCTTGTTGAGGTCCACC
Band lengths:
245-362
Functional annotations
There are 1 annotated functions for this event
PMID: 7583007
This event
Comparison of the integrin ITGA6 isoform alpha6AX1X2 (contains cassette exon X2 (HsaEX0032368)) with the alpha6AX1 isoform (lacks exon X2) using similarly transfected K562 cells showed no obvious differences between the alternative extracellular alpha6A isoforms with respect to ligand specificity and activation-dependency of ligand binding. After treatment with the anti-beta1 stimulatory antibody TS2/16, both the alpha6AX1beta1 and alpha6AX1X2beta1 integrin variants mediated cell adhesion to EHS tumor laminin (laminin-1), kalinin (laminin-5), human placental (laminin-2 and -4) and bovine kidney laminins. In contrast, the alpha6AX1beta4 and alpha6AX1X2beta4 integrins also mediated cell adhesion to laminin and kalinin without stimulation. Furthermore, the different transfectants did not differ in their ability to spread on kalinin. The presented data indicate that the X2 region in alpha6 is not involved in defining ligand specificity or affinity.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
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)