BtaEX0003084 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000000088 | ALCAM
Description
activated leukocyte cell adhesion molecule [Source:HGNC Symbol;Acc:HGNC:400]
Coordinates
chr1:50537555-50539988:+
Coord C1 exon
chr1:50537555-50537687
Coord A exon
chr1:50539543-50539581
Coord C2 exon
chr1:50539871-50539988
Length
39 bp
Sequences
Splice sites
3' ss Seq
ATTAACATTTTTCATTTCAGTAA
3' ss Score
7.01
5' ss Seq
GTGGTAGGT
5' ss Score
7.23
Exon sequences
Seq C1 exon
ACAGAGGAATCTCCGTATATCAATGGCAGGTATTATAGTAAAATTATCATTTCCCCTGAAGAGAATGTTACATTAACTTGCACAGCAGAAAACCAGCTGGAGAGAACAGTAAACTCCTTGAATGTCTCTGCTA
Seq A exon
TAAGTATTCCAGAACACGATGAGGCAGACGAGATAAGTG
Seq C2 exon
ATGAAAACAAAGAAAAGGTTAATGACCAGGCAAAACTAATTGTGGGAATTGTTGTTGGTCTCCTCCTCGCTGCCCTAGTTGCTGGTGTCGTCTATTGGCTATACATGAAGAAATCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000088_CASSETTE2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.089 A=0.714 C2=0.100
Domain overlap (PFAM):
C1:
PF139271=Ig_3=PD(43.8=77.8),PF142831=DUF4366=PU(27.0=66.7)
A:
PF142831=DUF4366=FE(11.7=100)
C2:
PF142831=DUF4366=FE(35.1=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGCACAGCAGAAAACCAGC
R:
AGCGAGGAGGAGACCAACAAC
Band lengths:
128-167
Functional annotations
There are 2 annotated functions for this event
PMID: 29453336
Loss of the membrane-proximal region of ALCAM (exon 13) increased metastasis four-fold. Mechanistic studies identified a novel MMP14-dependent membrane distal cleavage site in ALCAM-Iso2, which mediated a ten-fold increase in shedding, thereby decreasing cellular cohesion.
PMID: 32249828
[CRISPR screen]. This alternative exon is implicated in cell fitness by a CRISPR-based exon deletion phenotypic screen in RPE-1 cells.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development