RnoEX0045048 @ rn6
Exon Skipping
Gene
ENSRNOG00000001518 | Itga6
Description
integrin subunit alpha 6 [Source:RGD Symbol;Acc:621633]
Coordinates
chr3:58479417-58485573:+
Coord C1 exon
chr3:58479417-58479672
Coord A exon
chr3:58483970-58484086
Coord C2 exon
chr3:58485363-58485573
Length
117 bp
Sequences
Splice sites
3' ss Seq
TATGCCATGCACGTGACCAGGCC
3' ss Score
3.13
5' ss Seq
TAGGTTTGT
5' ss Score
4.07
Exon sequences
Seq C1 exon
ACGTGTGCGCATCGATACGAGAAACGGCAGCACGTTAACACGAAGCAGGAGTCCCGGGACATCTTCGGAAGGTGTTACGTCCTGAGTCAGAATCTCAGAATTGAAGATGATATGGATGGAGGAGACTGGAGTTTCTGTGATGGCCGATTGAGGGGCCATGAAAAATTTGGCTCTTGTCAGCAAGGAGTAGCGGCTACTTTCACTAAAGACTTTCATTACATTGTTTTTGGAGCCCCAGGGACTTACAACTGGAAAG
Seq A exon
GCCTGCTGTTTTTGACCAGCCTTTCTTATACAGACCCCGATCAGTTTGTTTATAAAACACGGCCTCCCAGGGAGCGGCCTGACACGTCCCCTGATGTGATGATGAATAGCTACTTAG
Seq C2 exon
GCTTTTCTCTGGACTCAGGGAAGGGTATTGTTTCTAAAGATGACATCACTTTTGTATCTGGTGCTCCAAGAGCCAATCACAGTGGGGCTGTAGTTTTGCTAAAAAGAGACATGAAGTCAGCACATCTTCTCCTTGAGTATATATTTGATGGTGAAGGCCTGGCTTCTTCGTTTGGCTATGACGTGGCGGTGGTGGACCTCAATGCAGATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001518_MULTIEX1-2/2=C1-C2
Average complexity
C3
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF135171=VCBS=PU(6.8=7.0)
Main Inclusion Isoform:
NA

Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTGGAGCCCCAGGGACTTA
R:
CCATCTGCATTGAGGTCCACC
Band lengths:
243-360
Functional annotations
There are 1 annotated functions for this event
PMID: 7583007
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]