Special

MmuEX0041127 @ mm9

Exon Skipping

Gene
Description
suppressor of cancer cell invasion [Source:MGI Symbol;Acc:MGI:2443716]
Coordinates
chr2:38988475-39045553:-
Coord C1 exon
chr2:39045509-39045553
Coord A exon
chr2:39005834-39005934
Coord C2 exon
chr2:38988475-38988606
Length
101 bp
Sequences
Splice sites
3' ss Seq
ACTTATTTTTTTTCACCCAGATT
3' ss Score
7.83
5' ss Seq
ATGGTAAAT
5' ss Score
6.41
Exon sequences
Seq C1 exon
ACTGTCTGGCACAGTGGAGAAACCACCCCGAAAACGGAAAAGCAG
Seq A exon
ATTTCTTAAGCAACTACTGTCTGACTACTGTCTGGAGATGAAGAAATTTTAAAACGACGTCTCTCTCCTCCTGGAGTTTTTGTTATATCTGGAGATAGATG
Seq C2 exon
GACTGAATTTACTCTTAAAGAAACTATGTCCTCTGGAGGTGCTGAAGATGACATCCCACAGGGAGAGAGGAAGACAGTTACAGATTTTTGTTATCTTTTGGATAAATCCAAGCAACTGTTCAATGGCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035236_CASSETTE2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.979 A=0.000 C2=0.444
Domain overlap (PFAM):

C1:
NO
A:
NO
C2:
PF120703=DUF3550=PU(2.8=31.1)


Main Inclusion Isoform:


Main Skipping Isoform:


Other Inclusion Isoforms:
NA
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCACAGTGGAGAAACC
R:
TTAAGCCATTGAACAGTTGCTTGG
Band lengths:
170-271
Functional annotations
There are 1 annotated functions for this event
PMID: 32736682
This study identified novel rat Scai variants 2 and 3 and characterized their functions in Neuro-2a cells. The novel Scai variants 2 and 3 contain unique exons that possess stop codons and therefore encode shorter proteins compared with the full-length Scai variant 1. SCAI variants 2 and 3 possess a nuclear localization signal, but do not have an MRTF-binding site. Immunostaining of green fluorescent protein (GFP)-tagged SCAI variants revealed a nuclear localization of variant 1, whereas localization of variants 2 and 3 was throughout the cytoplasm and nucleus, suggesting that other nuclear localization signals, which act in Neuro-2a cells, exist in SCAI. All three SCAI variants suppressed the neuron-like morphological change of Neuro-2a cells induced by a Rho effector, constitutively active mDia; however, the suppressive effects of variants 2 and 3 were weaker than that of full-length SCAI variant 1, indicating that the SCAI-mediated change toward a neuronal morphology appeared to be consistent with their nuclear localization. These findings indicate that generation of multiple SCAI splice variants fines-tune neuronal morphology.


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Pre-implantation embryo development
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types