DreEX0012577 @ danRer10
Exon Skipping
Gene
ENSDARG00000058538 | alcamb
Description
activated leukocyte cell adhesion molecule b [Source:ZFIN;Acc:ZDB-GENE-030131-1768]
Coordinates
chr15:19934338-19939381:+
Coord C1 exon
chr15:19934338-19934476
Coord A exon
chr15:19937445-19937474
Coord C2 exon
chr15:19939267-19939381
Length
30 bp
Sequences
Splice sites
3' ss Seq
ACTTTTATATCTGATTACAGTTG
3' ss Score
6.12
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
Exon sequences
Seq C1 exon
GTGAAATTTCAAGAGAGCGAACATGTGAATGGAAAGATCACATACTATATCACTGTCAGTCCAAAGGCCAATGTCACTGTGTCCTGCACAATCTCCAATGATTTGGGTTCTGACACGAGGAGCATCGATGTGTCGTCGC
Seq A exon
TTGTTGAGGACGTGACAATGGACAAACAAG
Seq C2 exon
ATCAGTCAGAGGACTACAGTGACCAGACGGCGCTGGCTGTTGGCATTGTTGTTGGCTTGATGCTGGCAGCACTTTTGATAGGACTGGCCTACTGGCTGTATATGAAGAAATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058538_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=0.136 C2=0.103
Domain overlap (PFAM):
C1:
PF138951=Ig_2=PD(55.0=93.6)
A:
NO
C2:
PF0103415=Syndecan=PU(58.7=94.9)
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:
CCAATGTCACTGTGTCCTGCA
R:
CCAACAACAATGCCAACAGCC
Band lengths:
127-157
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]