DreEX0012571 @ danRer10
Exon Skipping
Gene
ENSDARG00000026531 | alcama
Description
activated leukocyte cell adhesion molecule a [Source:ZFIN;Acc:ZDB-GENE-990415-30]
Coordinates
chr10:28850631-28854171:-
Coord C1 exon
chr10:28854042-28854171
Coord A exon
chr10:28851026-28851052
Coord C2 exon
chr10:28850631-28850745
Length
27 bp
Sequences
Splice sites
3' ss Seq
GATTTTATATCTGATTTCAGTAT
3' ss Score
5.58
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
Exon sequences
Seq C1 exon
GATGAAACATCGTATGTCAACGGAAAAGCCACATACAAACTGACGGTGGTCCCGAGTAAGAACCTCACCGTCAGCTGCCTCGTGACCAATAAACTCGGTTTCGACACAAAGGACATCAGCGTGTTTTCCC
Seq A exon
TATTTGAGGAGGACAAGCCCAAACCAG
Seq C2 exon
GAAAAAATGAAGATGGCGCAGACCAGGCCAAAGTGATTGTGGGTGTCGTGGTTGGACTGTTTCTAGCCGCTGCCCTGGTGGGACTCATCTACTGGTTGTATATCAAGAAAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026531_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.379 C2=0.171
Domain overlap (PFAM):
C1:
PF058086=Podoplanin=FE(27.9=100),PF139271=Ig_3=PD(40.0=68.2)
A:
PF058086=Podoplanin=FE(5.2=100)
C2:
PF058086=Podoplanin=FE(24.7=100),PF0103415=Syndecan=PU(55.4=79.5)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGGTCCCGAGTAAGAACCT
R:
CTGGTCTGCGCCATCTTCATT
Band lengths:
112-139
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]