MmuINT0139173 @ mm9
Intron Retention
Gene
ENSMUSG00000035236 | Scai
Description
suppressor of cancer cell invasion [Source:MGI Symbol;Acc:MGI:2443716]
Coordinates
chr2:38976631-38978610:-
Coord C1 exon
chr2:38978524-38978610
Coord A exon
chr2:38976730-38978523
Coord C2 exon
chr2:38976631-38976729
Length
1794 bp
Sequences
Splice sites
5' ss Seq
TTAGTAAGT
5' ss Score
7.79
3' ss Seq
AAAAAATTTTTTTCTTATAGTTT
3' ss Score
6.9
Exon sequences
Seq C1 exon
ACAAGTCTTGGATAATCGGTATGGCTTGAAGCGGTGGCAAATAGGGGAAATCGCTTCCAAGATCGGGCAGCTGTATTACCACTATTA
Seq A exon
GTAAGTGAATTTCATATGGAAAGAATAAAGTGTTTCTTTGGTTAAAACAGAGCATGTTGGAGGGAAGGCAGTGAGCTATAGATGGAATTTTGTTTAGGCTAGATGGATCAAGATGGCATCATGAAATGGCATTATATAATTTAAGCAGTATTCTTCATGTCAGCTGTTCTCTTCAGTAACTTCATTTGATCAGACCTGAGGAGTTTGATTTTGGTTTTTTTATAAGCAATGAATACTAAATAGATTTACCATTCTTAGGACTTCTCAAGTCTTGATAGTGTGTAGAGACATATAGCATATATGATGTTCATAGTATTCTTTACACACTCATCCTTGTTGACTATGTTTGAGAGGTTAAGTGAGGTAAATTGATAGTTGTTTGCATCCTTAAAATAGTAACATCTGAGACTGGAGAGAGAGCTCAGCAGTTAAGAGCACTGGCTGCTCCTTCTGAGATCCTGAGTTCAATTCCCACCAGCCACATTTTGGCTCACACCATCTGTAATGGGATCTGGTGCTCTCTTCTGATGTGTCTGAAGACAGCAACAGTGTACTTAGATACATAAAACTTTAGCCTTTTGTAATTTAAAAAGTAAGAAAAGAAAAACCCACAAAGCCCTTGATTGTGGCACACACCTTTTATCCCAGTACTCAGAAGGCAGAGGTAGGGGGAATTTCTGAGTTCAAGACCTGCCTGGTCTACATACAGAGTGAGTTCCAGGACAGCCAGGGCTAAACAGAGAAACCCTGTCTCAGAAAACCAAAGCAAGCCAAACAAAAGGTAAGAAAGTCATCGTCTTCCCAGTGTGGGCACGCCTCTTAGAATGCCCAGGACTCTTTCCCTCTTGTTGCCAGAAGAGGATCTTAAAAACCTTTGTTGCAGTGCTAAGAATAAGTGATTTTTGATGTACTCATCCCTAGAGAAGACATGGGTACCATCCTTTCCAAGCTTGGAGAACAGTAATTATGGAAGTACAGATAGAGAGAAGGGCTGAGAAGTACCAATCATTGTAATCATGAATCCTCAGCAACTACAGATGTCTTCGTTGGGTCTCCACTAAAAAGGGATCGTTAACAGCCAGAGCTTGATGGAAGAGGAGTCAGGGAGCTCTACTGATAGATTCAAAGAAAGGTTGTGTTTCTGTAGTTGTGTACCCACTGTTGCCCTCTCTAGGCTCCAGAGATAGTCCCAATCCAATGGTTGCATAAATGGCTCTGGTTAAACTAAATGAGACATACAACAAAACCATGTCATGAATCTGGAAAAGGAACAGGAAGAAAGAAGACTTGATAGGAGTAGAAAGATGAGAGAGAGAGGAGAGAGTAACCAGAAGGGTAGGTGGGTGGGTGTGTATAAAATTTGTCAGGGTACTAAATAAACTTTTTAAAGTAAATTATTTTTTGAAAGTCTCTTATTAAACTAGACATGTTAAACAGGCATCATAGCTAATTTGCATTCCCCAAAGTAGTAGTTTAGTAAGGAGGGGAAAAAACTAAAGAAATGGACCAAAGATCAAGTGACAGTAGGTTAGTCGAGTTCTGGAAGCAGGCATAGTAGAATCCTGTCCCTTTTACAATGAGAGTGATGTGTACTTTGGTTGGAACAGCACGGAAGAACTGTATTGCTGCTGTTACCAGACAATTGAAAGATAACAAGGTCGGATACCTTGCTGACTCAAAGTGAAGGCAGTCATTCCCATCCCCCTGTGCAGGGCAGGGCAATCTAGAACAAGTGTTTTTCATGAGCATTACACCCAGTTTGCGTCTTACTTAAAAAAAATTTTTTTCTTATAG
Seq C2 exon
TTTACGAACTTCTGAGACCAGTTATCTGAATGAGGCTTTCTCCTTCTACTCTGCAATCAGACAGAGATCATACTACTCTCAAGTCAATAAAGAGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035236-Scai:NM_178778:5
Average complexity
IR-S
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(5.8=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:
AGTCTTGGATAATCGGTATGGCT
R:
TGTCCTCTTTATTGACTTGAGAGT
Band lengths:
182-1976
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: