Special

MmuEX6099746 @ mm10

Exon Skipping

Gene
Description
SEC16 homolog A, endoplasmic reticulum export factor [Source:MGI Symbol;Acc:MGI:2139207]
Coordinates
chr2:26412836-26415401:-
Coord C1 exon
chr2:26415307-26415401
Coord A exon
chr2:26414371-26414445
Coord C2 exon
chr2:26412836-26412913
Length
75 bp
Sequences
Splice sites
3' ss Seq
CATTTCATATTTCCTTATAGGTG
3' ss Score
10.53
5' ss Seq
GAGGTAGGG
5' ss Score
7.81
Exon sequences
Seq C1 exon
ATGCAGAAGAGCCACAACCTGCAGATGGGACTGGCTGTAGGGGACAGGCACCAGCTGGGACTCAGTCTAAGGCAGAGTCCACCCTGGAACCCAAG
Seq A exon
GTGGGAAGTTCTACAGTATCAGCCCCTGGACCTGAGCTCTTACCCTCCAAACCAGATGGCTCCCAAGGAGGAGAG
Seq C2 exon
GCTCCTGGAGACCATTGTCCTACAGGGGCCCCTCATGGTGGGTCTGTGCCCTTTTACAACCCTGCTCAGTTGGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026924-'49-60,'49-57,52-60=AN
Average complexity
A_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=0.981
Domain overlap (PFAM):

C1:
NO
A:
NO
C2:
NO


Main Inclusion Isoform:


Main Skipping Isoform:
NA


Other Inclusion Isoforms:


Other Skipping Isoforms:
NA
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGCAGAAGAGCCACAACCTG
R:
CACCAACTGAGCAGGGTTGTA
Band lengths:
170-245
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]


SPECIAL DATASETS

  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types