MmuINT0003451 @ mm10
Intron Retention
Gene
ENSMUSG00000043183 | Simc1
Description
SUMO-interacting motifs containing 1 [Source:MGI Symbol;Acc:MGI:2442599]
Coordinates
chr13:54539704-54541552:+
Coord C1 exon
chr13:54539704-54539856
Coord A exon
chr13:54539857-54541423
Coord C2 exon
chr13:54541424-54541552
Length
1567 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGG
5' ss Score
5.19
3' ss Seq
CTCCTGTGTTCTGGATCCAGGAT
3' ss Score
8.05
Exon sequences
Seq C1 exon
AGATGTTATTAAGTGGCTGGTCAAAGCAGTGACTGAAAATGAATTAACTCCACCCCAAGATGAGACTCAGACCTCTCCAAGAACAGGAGTCTTGAAAACTAGCAGTGACCATCTGTCTCCCCGGCCTAACCAGAACAAGAACACCAATCAACT
Seq A exon
GTAAGGAGCAAGCAAAGAATTGTCTCCAGGGCTTTGAGGATTTGGTATCTAGCAAATAGGACTGTCCTAAGAACAGATTGCTCCAAATTACCAACTATTGTAACATAGACTTTTTCTCAAAAAAAAAAAAAAAAAAAAAAGGAAAAGAAAAAAGGACTTATCTAGGTTAGGAGTGTAATTTTGTAGAATTCGTGTGTGGCATACACTAGGACCTACATTCCATCCACAGAAAAGAAGGGGCTCTCACTGCTAACCTTCCACCTTTGGGTTCTGATCAGAAAGGGTCCCCTCTTTCTAGCTCCCTTTTGTGGATACTAACCCAAGTCCAGAGCCTGCTCTGCCGGACATTGCTTCCTCTAAAGACACCCATCCCACGTAGCCATTCAGACTTGCACTGAGGAGCAGTCCTGCCCCTTGAGACTTGTAACTCTGATCCATCTCCTACCTCCTAGCTGCTGAGACCTCCAGCTCTGTTGTCTTCTTTTAAACACTAATGAAATTGACTTGATCAACTTGAACAGAGCCGGTATAGCAGCTCACAGGTGTCTTCATCGAAGTCAGAAGCTGGCCTGCCCTGTTCTGTTATCTGGTCACTGTCTGCAGTTTCTCTGAAAACAACACACTTCCACCATATAATATGTGCTTAAGTGAGTGCTGTCAAGCCAAGCTTACCCTTCTGAAGTGTTGCTTAGCCTCCCAGTGCTGTGTCTGCCTCTCTCCCATATTTGTGTCTGATGGGAGAGAAGGTGAGGTCTACCACTGGAAATTCTGAGGCTAGTCTTAGTAAGAAACCACTAATAGGACATATACATGATGAGGCTGGAGAGATGGCTTAGCAGTGAGAGTACCGACTGCTCTTCCAGAGGAACTTGGTTCCCAGCACCCACACAGCAGCTCCGAACCATCTGTAACTCCATTTGCAGGAGATCTAGGGCCTTTGTTGGTCTGTGACAGCACCAGGCATGCACATGAAGCATAGAAGTATTTAATATGTTAAAAAAAAAAAGTAATTGAAATGTCTTCTATAACAAAGAGAATAATGTTAGTCACCTTAGACCTGTTTTTTCATTTCCCAAATAGAGAAGTTACAGCGTCTTTACAGTTCTCTAGACCCTTAGGATTATATTGTTCTGTTTTAATTTAAGAGTATCTTGCTCATGTAGCTCACCCTCAAATTCTAGAAGTTTCACATATGAGCTGGCAGAGAGAATCAGAAGGATGGACTACTAAGCGGGAATGAGCTAAGGGCTGGGTACTCTCCTTGGCCTGTGTATTGTGAGGACCTTGTAATGGTCTCTGTTCTGTTGTTGTTGTTGTTGTTGTTGTTCACTTTTTTGTTGTTTGTTTTAAGATAAAATCTCAACGGTAACTCTAACTGGCCTGAAACTCAGTACATAGATCAGGCTGGCCTGCCTGTCTCTACCTTCTGAGTGCCAGAATTAAAGGTGTGTACCTGCACACCCAGTTGTCTCTGTGCTTGGCATACTCTTGTGGGGACCTTCTCCAGCTTCAGGAAAGCCTCTCTCCATGTCTTCCTACTCATGTGTCTCCTGTGTTCTGGATCCAG
Seq C2 exon
GATTGTGTGTCAGCTTCAGAGGATGTTGTCCATCGCTGTAGAGGTGGACAGGACTCCAACCTGCAGCTCCAATAAAATAGCGGAGATGATGTTTGGGTTTGTGCTGGATATCCCTGAGAGGAGCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043183:ENSMUST00000121401:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.604 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
NO
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTATTAAGTGGCTGGTCAAAGCA
R:
CTCTGGCTCCTCTCAGGGATA
Band lengths:
279-1846
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