BtaEX0018501 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000012897 | ITGA7
Description
integrin, alpha 7 [Source:HGNC Symbol;Acc:HGNC:6143]
Coordinates
chr5:57895844-57898519:+
Coord C1 exon
chr5:57895844-57895969
Coord A exon
chr5:57896949-57897061
Coord C2 exon
chr5:57897957-57898519
Length
113 bp
Sequences
Splice sites
3' ss Seq
CCTCCTCCCTTATATCCCAGTGT
3' ss Score
8.49
5' ss Seq
GGGGTAATT
5' ss Score
5.8
Exon sequences
Seq C1 exon
ATCCCGGTGATGGTGTACCTGGACCCCGCGGCTGTGGCAGCAGAAGGAGTCCCCTGGTGGGTCATCCTGTTGGCTGTACTAGCCGGGCTGCTGGTATTGGCGCTGCTGGTGCTGCTCATGTGGAAG
Seq A exon
TGTGGCTTCTTCCGTCGGAGCAGCCAGAGCTCATCTTTTTCCACCAACTATCACCGGGCCCGGCTGGCTGTGCAGCCCTCAGCTGTGGAAGCTGGGGGTCCAGGGACTGTGGG
Seq C2 exon
ATGGGATTCTTCAAGCGAGCGCGGTACCCCGAAGCCACCGTACCCCAGTACCATGCGGTGAAGATCCCGCGGGAAGACCGGCAGCAGTTCAAGGAGGAGAAGACGGGTACCATCCTGAGGAACAACTGGGGCAGCCCCCGGCGGGAGGGCCCAGATGCCCACCCTATCTTGGCTGGGGATGGGCACCCAGAGCTGGGCTCTGATGGGCACACAGTGCCAGGCACAGCTTAGCCTTCTCCACCTGGCCTGGCCCATAGGCCCCTTGCACCCCTTCCCCAGATATGGCTCCTGGGGATGACGAGGGTAGAATGGGTTACTGGTGTCCCATCCAGATTTGGCAGGATCTCTTTCCTCTGGGGCACAGATCTCTGTCCCCCATGAGGACCACCCCCCTGCCAAACTTCCCCTTATGATGCTGTGAGATGAAAGGGGGTAAATCAGGGATGGGTCGTGGGGGAGGGTGAGAAGGGCAGCGGTGTCCTGATTCAAAAGTGGGGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012897_CASSETTE2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.079 C2=0.594
Domain overlap (PFAM):
C1:
PF0035715=Integrin_alpha=PU(0.1=0.0)
A:
PF151761=LRR19-TM=FE(49.3=100)
C2:
PF0035715=Integrin_alpha=PD(86.7=16.9)
Main Inclusion Isoform:
ENSBTAT00000017145fB3499
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGTCATCCTGTTGGCTGTA
R:
CATCCCCAGCCAAGATAGGGT
Band lengths:
250-363
Functional annotations
There are 2 annotated functions for this event
PMID: 10094488
Two-yeast hybrid assay was used to examine interaction between various alpha integrins (including splice isoforms of integrin alpha 3 (alpha3A and alpha3B (these differ in presence of penultimae exon HsaEX0032352 (present in A, absent in B)), splice isoforms of integrin alpha 6 (alpha6A and alpha6B) (these differ in the presence of penultimate exon HsaEX0032370 (present in A, absent in B), and splice isoforms of integrin alpha 7 (alpha7A and alpha7B (these differ in presence of penultimate exon HsaEX0032377 (present in A, absent in B)) and four proteins, two of which are described as clones as they were identified in a cDNA screen (Mss4, BIN1, clone 63, and clone 80).
PMID: 10694445
HEK293 overexpressing integrin alpha 7 isoforms alpha7A (contains penultimate exon (HsaEX0032377)) or alpha7B (lacks penultimate exon) are shown to adhere to similar extends to laminin-1, a fragment of laminin-1, and laminin-2. Migration across surfaces with above mentioned laminins is also similar. Overexpression of either integrin alpha 7 isoform negatively affects surface expression other beta1-integrin associated alpha integrin chains (alpha1, alpha3, alpha5, and alpha6). Overexpression also lead to reduced adhesiveness for both isoforms. Note, while they state that the isoforms behave similarly, I do think that their data points toward differences.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development