HsaEX0003574 @ hg19
Exon Skipping
Gene
ENSG00000170017 | ALCAM
Description
activated leukocyte cell adhesion molecule [Source:HGNC Symbol;Acc:400]
Coordinates
chr3:105268971-105271429:+
Coord C1 exon
chr3:105268971-105269103
Coord A exon
chr3:105270988-105271026
Coord C2 exon
chr3:105271312-105271429
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
ACAGAGGAATCTCCTTATATTAATGGCAGGTATTATAGTAAAATTATCATTTCCCCTGAAGAGAATGTTACATTAACTTGCACAGCAGAAAACCAACTGGAGAGAACAGTAAACTCCTTGAATGTCTCTGCTA
Seq A exon
TAAGTATTCCAGAACACGATGAGGCAGACGAGATAAGTG
Seq C2 exon
ATGAAAACAGAGAAAAGGTGAATGACCAGGCAAAACTAATTGTGGGAATCGTTGTTGGTCTCCTCCTTGCTGCCCTTGTTGCTGGTGTCGTCTACTGGCTGTACATGAAGAAGTCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170017_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
Show structural model
Features
Disorder rate (Iupred):
C1=0.127 A=0.625 C2=0.087
Domain overlap (PFAM):
C1:
PF138951=Ig_2=PD(48.9=95.6),PF146101=DUF4448=FE(31.0=100),PF058086=Podoplanin=FE(37.9=100),PF142831=DUF4366=PU(27.0=66.7)
A:
PF138951=Ig_2=PD(0.1=0.0),PF146101=DUF4448=FE(9.3=100),PF058086=Podoplanin=FE(11.2=100),PF142831=DUF4366=FE(11.7=100)
C2:
PF146101=DUF4448=FE(27.5=100),PF058086=Podoplanin=FE(33.6=100),PF142831=DUF4366=FE(35.1=100)
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACAGCAGAAAACCAACTGG
R:
GCAAGGAGGAGACCAACAACG
Band lengths:
124-163
Functional annotations
There are 2 annotated functions for this event
PMID: 29453336
This event
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
This event
[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
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)