MmuINT0003448 @ mm10
Intron Retention
Gene
ENSMUSG00000043183 | Simc1
Description
SUMO-interacting motifs containing 1 [Source:MGI Symbol;Acc:MGI:2442599]
Coordinates
chr13:54528304-54529223:+
Coord C1 exon
chr13:54528304-54528536
Coord A exon
chr13:54528537-54529153
Coord C2 exon
chr13:54529154-54529223
Length
617 bp
Sequences
Splice sites
5' ss Seq
ACAGTATGA
5' ss Score
2.27
3' ss Seq
TGATGTCACTTGACTTTCAGGCT
3' ss Score
6.84
Exon sequences
Seq C1 exon
AGCAAGGGTCAGAAATTAGAACCCATCCCTCATCGAAGACTAAGAATGGTGACAAACACTATTGAAGAAAACTTCCCTTTGGGGACTGTGCAGTTTTTAATGGACTTTGTTTCACCCCAACATTACCCACCCAGAGAAATTGTGGCTCACATCGTCCAGAAAATCCTGCTCAGTGGCTCTGAGACTGTGGATGTCCTCAAGGAGGCCTACATGCTTCTCATGAAAATCCAACA
Seq A exon
GTATGAACCATTACAGTGGGTTGGCCAAGTCTTCTAGGGAACCTAGACTCAGGGCACAGCTTCCCTGTCTAAGCTTTGATTCAGCTGGCCTGGCAGCTTCCTTAAGAATGCTAATTGCAAGTAGCAAGGAACCTAATAAAACCTGCGTCAATTGCTAGCAAAAGAATGTAATGACTTATTTTCACTAGAAATCTGGGAATGCTATTTGATACTGTTTTCATAAATGGCTGCTTGGACCCAGTTTGCAACCCTGCCTTGGTTCTATAGTCCTTATCTTCAGATTTTTATAGTATTTTGGGTTAGAAAATCAACTTCAGTAATTACACAAGCCGAGTTGTATTATAATTGGGTTAACATGACAGGAGTCCATTTTTAGACATTCATAGTGAATTAAAGAATAGGATATTGTGATTGGCTCAACGAGTCACATGCTTCATGTAGTCCTGATAGGTATAGCTCTCTGGCAATGAGCTGGCCTCGACTGACATGCTGTGGTCCTGAAGGGTAGGTCAGGTTGCTTATGATAAGAAGAGGCTTTTTGTCCTGTCACCTTCCAGATCCTATCCTTTCTGTCACTAAAATCTCCAGAATTCTAATTGATGTCACTTGACTTTCAG
Seq C2 exon
GCTGCATCCAGCCAATGCCAAGACAGTGGAGTGGGACTGGAAACTGCTCACCTATGTCATGGAGGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043183:ENSMUST00000121401:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.115 A=NA C2=0.118
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCAAGGGTCAGAAATTAGAACCC
R:
TCTTCCTCCATGACATAGGTGAGC
Band lengths:
302-919
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