MmuINT0139168 @ mm10
Intron Retention
Gene
ENSMUSG00000035236 | Scai
Description
suppressor of cancer cell invasion [Source:MGI Symbol;Acc:MGI:2443716]
Coordinates
chr2:39080077-39080547:-
Coord C1 exon
chr2:39080374-39080547
Coord A exon
chr2:39080178-39080373
Coord C2 exon
chr2:39080077-39080177
Length
196 bp
Sequences
Splice sites
5' ss Seq
TAGGTACCC
5' ss Score
5.35
3' ss Seq
CTGTTGCTTCCTCTCTGCAGATC
3' ss Score
12.57
Exon sequences
Seq C1 exon
ATCAGTCTCAGCGAGGTAGCCTCTTCACGCTCTTTTTGAACAATCCTCTAATGGCCTTCCTATTTGTGTCTGGATTGTCAAGCATGCGTAGAGGCCTGTGGGAAAAGTGTCAAGAATATCTTCGAAAAATCAACCGTGATATTGCCCAGCTACTGACCCATTCACGTTCAATAG
Seq A exon
GTACCCTGTTAATCTACCTGAACACTTAACCAAAGCTTACTGTAGTGGCTTAAATGGTTTCCTGCTATGTATTGTATAGGTTTTTTTAAAGGTACTTATCCCAGATATGAAAGTCATGAAGCCTTTCCTTAACTTAGTTTCCTATTGAAGTGTCATTTTCATGTCACCTCCTTTCACTGTTGCTTCCTCTCTGCAG
Seq C2 exon
ATCAGGCCTTCCTCCAGTTTTTTGGAGATGAATTTCTTCGATTGCTTCTCACAAGGTTTGTCTTCTGTTCAGCCACCATGAGGATGCACAAGGCCTTTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035236:ENSMUST00000038874:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF120703=DUF3550=FE(11.7=100)
A:
NA
C2:
PF120703=DUF3550=FE(6.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTAGCCTCTTCACGCTCTT
R:
AAGGCCTTGTGCATCCTCATG
Band lengths:
258-454
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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