RnoEX0078967 @ rn6
Exon Skipping
Gene
ENSRNOG00000019122 | Sec16a
Description
SEC16 homolog A, endoplasmic reticulum export factor [Source:RGD Symbol;Acc:2322350]
Coordinates
chr3:3859885-3862363:-
Coord C1 exon
chr3:3862269-3862363
Coord A exon
chr3:3861540-3861617
Coord C2 exon
chr3:3859885-3859962
Length
78 bp
Sequences
Splice sites
3' ss Seq
CACTTTATATTTCCTCATAGGTG
3' ss Score
9.62
5' ss Seq
GAGGTAGGG
5' ss Score
7.81
Exon sequences
Seq C1 exon
ATGCAGAAGAGTCACAACCTGCAGATGGGACTGGCTGTAGGGGACAGGCACCAGCTGGGACTCAATCTAAGGCAGAGCCCACCCTGGAAGCCAAG
Seq A exon
GTGGTAAGCTCTACAGTATCAGCCCCTGGGCCTGAACTCTCACCCTCCAAACCAGCAGATGGCTCCCAGGGAGGAGAG
Seq C2 exon
GCTCCTGGAGACCACTGTCCTGCAGGGGCCACTCCTGGTGGGTCTGTGCCCTTTTACAACCCTGCGCAGTTGGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019122-'39-47,'39-43,40-47
Average complexity
C1
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=1.000 C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCAGAAGAGTCACAACCTGC
R:
CCAACTGCGCAGGGTTGTAAA
Band lengths:
167-245
Functional annotations
There are 1 annotated functions for this event
PMID: 27492621
Activation-induced alternative splicing of Sec16a (inclusion/exclusion of HsaEX0056828 and/or HsaEX0056829) controls adaptation of COPII transport to increased secretory cargo upon T-cell activation. Using splice-site blocking morpholinos and CRISPR/Cas9-mediated genome engineering, the authors show that the number of ER exit sites, COPII dynamics and transport efficiency depend on Sec16 alternative splicing. As the mechanistic basis, the authors suggest the C-terminal Sec16 domain to be a splicing-controlled protein interaction platform, with individual isoforms showing differential abilities to recruit COPII components. These work connects the COPII pathway with alternative splicing, adding a new regulatory layer to protein secretion and its adaptation to changing cellular environments.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]