Special

RnoEX0078284 @ rn6

Exon Skipping

Gene
Description
suppressor of cancer cell invasion [Source:RGD Symbol;Acc:1594720]
Coordinates
chr3:23421455-23473492:-
Coord C1 exon
chr3:23473448-23473492
Coord A exon
chr3:23450535-23450630
Coord C2 exon
chr3:23421455-23421586
Length
96 bp
Sequences
Splice sites
3' ss Seq
TTACTTATTTTTTCACCCAGATT
3' ss Score
7.7
5' ss Seq
ATGGTAAAT
5' ss Score
6.41
Exon sequences
Seq C1 exon
ACTGTCTGGCACAGTGGAGAAACCACCTCGAAAACGGAAAAGCAG
Seq A exon
ATTTCTTAAGCAACTACTGTCTGACACTGGAGATGAAGAAATTTTAAAATGAAGTCTCTCTCCTCCTGCAGTTTTTGTTATATCTGGAGATAGATG
Seq C2 exon
GACTGAATTTACTCTTAAAGAAACCATGTCCTCTGGAGGTGCTGAAGATGATATCCCACAGGGAGAGAGGAAGACAGTTACAGATTTCTGTTATCTTTTGGATAAATCCAAGCAACTGTTTAATGGCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025278_MULTIEX1-1/2=C1-2
Average complexity
S*
Mappability confidence:
100%=100=100%
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=1.000 A=0.647 C2=0.444
Domain overlap (PFAM):

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


Main Inclusion Isoform:
ENSRNOT00000039410fB12931


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
AGCCATTAAACAGTTGCTTGGA
Band lengths:
167-263
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]