GgaEX6027656 @ galGal3
Exon Skipping
Gene
ENSGALG00000000406 | F1NRZ0_CHICK
Description
NA
Coordinates
chr28:525397-527896:+
Coord C1 exon
chr28:525397-525489
Coord A exon
chr28:527399-527527
Coord C2 exon
chr28:527790-527896
Length
129 bp
Sequences
Splice sites
3' ss Seq
ACTCTGTCTTCTCCTTGCAGGAC
3' ss Score
13.24
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
Exon sequences
Seq C1 exon
CCTCTCCTGCCCGCACTGGGCTGGTTCTACCTGCTGGAGCTCTCCTTCTACTGCTCACTGGTTGTCACCCTGCCCTTCGATGTGAAGAGGAAG
Seq A exon
GACTTTAAGGAACAGATCATCCACCACATTGCCACCATCACTCTGATCTTTGTATCCTACTGTGCCAACCTGATACGGCTTGGGGTGATGATCATGCTGATCCACGATGCCTCCGATTACCTTCTAGAG
Seq C2 exon
TTGGCCAAGGTTCTCCATTACATGAAATGGAAGCGGGTCTGCGAAGCGGTCTTTATTGTTTTCGCTGTGGTGTTCATCAGCTCCCGCCTTGTCATTTTCCCACTAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000406-'5-6,'5-5,6-6=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0379811=TRAM_LAG1_CLN8=FE(15.5=100)
A:
PF0379811=TRAM_LAG1_CLN8=FE(21.6=100)
C2:
PF0379811=TRAM_LAG1_CLN8=FE(18.0=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCCTGCCCGCACTGG
R:
AGTGGGAAAATGACAAGGCGG
Band lengths:
196-325
Functional annotations
There are 1 annotated functions for this event
PMID: 33568634
Differential AS-based survival analysis shows that this AS event of CERS2 is a poor prognostic factor for Luminal B patients. As Exon 8 corresponds to catalytic Lag1p domain, overexpression of AS transcript of CERS2 in Luminal B cancer cells leads to a reduction in the level of very-long-chain ceramides compared to overexpression of protein-coding (PC) transcript of CERS2. The authors further demonstrate that this AS event-mediated decrease of very-long- chain ceramides leads to enhanced cancer cell proliferation and migration. Therefore, these results show subtype- specific AS of sphingolipid genes as a regulatory mechanism that deregulates sphingolipids like ceramides in breast tumors, and can be explored further as a suitable therapeutic target.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]