Special

DreEX0040095 @ danRer10

Exon Skipping

Gene
Description
integrin, alpha 6b [Source:ZFIN;Acc:ZDB-GENE-050320-5]
Coordinates
chr1:30232585-30237595:+
Coord C1 exon
chr1:30232585-30232846
Coord A exon
chr1:30234813-30234929
Coord C2 exon
chr1:30237382-30237595
Length
117 bp
Sequences
Splice sites
3' ss Seq
TCTTGTTTGTGCAACTGTAGGTG
3' ss Score
7.08
5' ss Seq
TAGGTTTGT
5' ss Score
4.07
Exon sequences
Seq C1 exon
GTCTGTGCACATCGATACCAGCGGCGCTTATTTGTTGGCTCAGTTCAGGAACTGCGTGACTTGACAGGTCGGTGCTATGTACTTAGTGAGGATGTGACGATTAATGAGATCTCAGATGAAGATGGAGGGGATTGGATGTTCTGCAATGGGAGAAACAGAGGGCACGAGCGGTTTGGATCATGCCAGCAGGGCATGTCCGCCACATTCACAAAGGACTATCACTATCTGGTGTTTGGAGCACCAGGCGCTTACAACTGGAAAG
Seq A exon
GTGTTCTGTTCTTGACTAGCATATCCAGTAACCATCCTGATCAGTTTGTGTATCAGTCACCTCCCCTTCAGGTGCCAAAGGAGAATGTTTCTTATGTGGCATCAAATAGCTATTTAG
Seq C2 exon
GTTTCTCTTTGGATTCTGGAAAAATGCTGACTAAGAGAGGTCAGTTGACCATAGTTGCTGGGGCTCCAAGAGCCAATCACAGTGGGGCAGTTGTGCTTTTAAAGAAGGATGAGGCTAAATCCTCCTTGTTGACGGCTGAGTACACCCTAGAGGGTAGTGGACTTGCCTCTTCCTTTGGTTATGACCTTGCAGTGCTTGACATCAATGGAGATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069946_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=0.000 A=NA C2=0.000
Domain overlap (PFAM):

C1:
NO
A:
NA
C2:
PF135171=VCBS=PU(25.0=31.9)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal4)
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCGCCACATTCACAAAGGAC
R:
ACCAAAGGAAGAGGCAAGTCC
Band lengths:
246-363
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]