MmuINT0148352 @ mm9
Intron Retention
Gene
ENSMUSG00000056427 | Slit3
Description
slit homolog 3 (Drosophila) [Source:MGI Symbol;Acc:MGI:1315202]
Coordinates
chr11:35472841-35474851:+
Coord C1 exon
chr11:35472841-35472912
Coord A exon
chr11:35472913-35474687
Coord C2 exon
chr11:35474688-35474851
Length
1775 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
CTTCCTCTTCTGCCTTCCAGGGC
3' ss Score
11.7
Exon sequences
Seq C1 exon
GACCCTCCATGGAAATGACATTTCCAGTGTTCCTGAAGGCTCCTTCAATGATCTGACATCCCTTTCCCACCT
Seq A exon
GTAAGTAGCCTCTTCCTTAAGGTACATTGGCTCAAAACAGAACATGGTAATGGTGACAGTCATCACTTTGTGTATATTCTGTCCTCGTGTTAGGCATTTGGCCATCCGTATGCACAGGGAACTAGCTCCAGGAGCCCCAGTAACCCACAAATGCTCAAGTCACTTATGTACAGTGAGATGGCATATGTGTCCAACACCACACATTCTCCTGTGTGCTTGACATAGTCTCTGGAGTACTTAAGATACCTAGTACGACTGTAAATTCTTTGTACATAATGGTTATATTATTTTGAGTGTGGAATAAGGACCCCAAAATTGTCCAGGTTTATATGTATTCACTACATGTAAAACTTTGAAAAATTATTTTTGACCCATAGTTGGTTAGACTTGCAAACAGGAAACCTGAGATTCAGAAAATGAAAGGGGCTTTGTTTTGAAATACTGTATTCAAACTGTTCACAAAGGTTTTGTTTCAGAAGCCTTCAAAGACATCTGACCTGTCACATAGTGACATAGTGTTTGGACCCTTTCTATACCCTAAACACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGTTTTTCGAGGCAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCTCCTCCTTCTGCCTCCCAAGTGCTGGGATTAAAGGTGTGCGCCACCACCACCTGGCTACCCTAAACACTTTTGATGAATTATCTCTTATATTTTTTTTTACGGAATTAAGGTGCTTTATTCTCTTATATATGATGAAATTCAGACTCAGGAAAGTTAAAGTATTTTTCCTGAGGCTGCACAGCCCACAGGTAGGCAGCTACGTGTTTGCCTTGACTCCGGTGGGCATATTATCAGCCATGCTGTATTCCTTTCTTATTCCACTCACGGAACTTGAGAGCATGAACGATAGCCTCTCATCAAGCCGTGAGACTTTACCTAGAGCTCAGTCCCCTGACTCCCAGGCCAGCCCTGTGTCCATAGCTAGCACTCTCAGACAGTGTCCATAGCTAGCACTCAGACAGTGCCCAGGCACCCACCTCTGTTGGTAAGATGGTAAGACTGTATTCCTCCTCTGTATACATTTTAATTATTTTCATGTTGTATACACAGGCTACAGTACTGACATGTATGCATTCTGTACACCAAAAGTAGAAATAGTAGATAATAGGATATTTTAAAAAATGAATTGTACTGTTTTCTTCCCAATCACTTTGGAGAAGTTTGGGGTGAGCTATGGCTCACCCCCATATCTTCAATCTCCCCGACTTGAAGCTGCTTCCTGAATAGGGGTCCTGGAACAACTCTTTGAGAACAAATCTTCTAACAGACCCTTTGCTTGAGAGTCACATGAGGAGGTGGCCAGAGGTCTGGAATGTGTCCCTTGGAGAGCCAGGACTATAGGAGAGTCCAGGACAGAATGTTCCAGAGCATCAAGAACAAAGCCTCAGAAGTGGCTGCCATTGCTGAAGGGCACAGACATCACTCTGTCTAGAGCAGTCACTTAGGCGCAATGGAACATCTACTGAATTGGAAATAGACTCTGGAAACTTTGATTTTTTTTTTCTTAGTGGAGATGTATCTTCTAGCCTGCACACTAGACTCCTCTAATTTAGTTTTAAAACCTTGAGTTTTCAGAGAGCCACAGATGGGGAGGAGCCTGTGGGCCAGGCCAGGCCAGGCCAGGCCAGGCAGGGCCTAACTTCCTCTTCTGCCTTCCAG
Seq C2 exon
GGCCCTGGGAACCAACCCTCTCCACTGTGACTGCAGTCTGCGTTGGTTATCAGAGTGGGTAAAGGCTGGATACAAGGAGCCTGGCATTGCCAGATGCAGCAGCCCCGAGTCCATGGCAGACAGACTCCTGCTCACCACCCCCACTCACCGGTTCCAGTGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056427-Slit3:NM_011412:24
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:
PF138551=LRR_8=PD(11.5=28.0)
A:
NA
C2:
PF0146319=LRRCT=WD(100=46.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCCTCCATGGAAATGACAT
R:
ACTGGAACCGGTGAGTGGG
Band lengths:
230-2005
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: