MmuINT0139176 @ mm10
Intron Retention
Gene
ENSMUSG00000035236 | Scai
Description
suppressor of cancer cell invasion [Source:MGI Symbol;Acc:MGI:2443716]
Coordinates
chr2:39106920-39107306:-
Coord C1 exon
chr2:39107208-39107306
Coord A exon
chr2:39107073-39107207
Coord C2 exon
chr2:39106920-39107072
Length
135 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATT
5' ss Score
8.88
3' ss Seq
TGTGCTTCTTTTTTCTTCAGGCA
3' ss Score
10.87
Exon sequences
Seq C1 exon
GAATTGTCTGATGAAATTGAAGATTATACTCATCGCTTTAATACTGAAGATCAAGTCGAGTGGAACCTGGTGCTTCAAGAGGTAGCAGCATTCATTGAG
Seq A exon
GTAATTTCTTGAGAGAAAGCTTGTCACCGTCATAGGTAGGCAAGTGACTATGCTGTGTTTATTGTATGTATGTAACTTTGAGAAGAACAAGAAGTGATATTCTGTGTTACATTAATGTGCTTCTTTTTTCTTCAG
Seq C2 exon
GCAGACCCTGTGATGGTGTTAAATGATGATAACACTATTGTTATCACATCCAATCGCCTCGCTGAGACAGGAGCCCCCTTGCTGGAGCAAGGCATGATTGTGGGACAGTTGTCTCTGGCTGATGCACTCATTATTGGTAATTGTAATAATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035236:ENSMUST00000038874:8
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(6.5=100)
A:
NA
C2:
PF120703=DUF3550=FE(10.1=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:
TGAAATTGAAGATTATACTCATCGCT
R:
ACCAATAATGAGTGCATCAGCCA
Band lengths:
226-361
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