MmuINT0090033 @ mm9
Intron Retention
Gene
ENSMUSG00000015714 | Lass2
Description
LAG1 homolog, ceramide synthase 2 [Source:MGI Symbol;Acc:MGI:1924143]
Coordinates
chr3:95123984-95124681:+
Coord C1 exon
chr3:95123984-95124157
Coord A exon
chr3:95124158-95124563
Coord C2 exon
chr3:95124564-95124681
Length
406 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGC
5' ss Score
3.2
3' ss Seq
TTCTCATGTCCCTTACTCAGTTA
3' ss Score
6.26
Exon sequences
Seq C1 exon
GATGCTCCAGACCTTGTATGACTACTTCTGGTGGGAACGACTATGGCTGCCTGTGAACTTAACCTGGGCTGATCTAGAAGACAAAGATGGACGTGTCTATGCCAAAGCCTCAGATCTCTACATCACACTCCCCCTGGCCCTGCTCTTTCTCGTCATTCGATACTTCTTTGAGCT
Seq A exon
GTGAGCATGCCCTCAAACCTTCTCTGGTTGTCAGCCAACCTATAGGGCTTCGTGTTGGTCTTCTGATACTTAGTTCTGGACATTGGTGTTCTGGCCACTCAGGAGCCCATGCTCCCCCTCCCCCAGCGCACCATTGTCTTCCTGAGGCTGAGGACTCAGCATCCCCAGCCTTGTCCTTCAATGGTTTTTTGTTTTCATCCTGCACCCGCCTCCTCGCCTGGTCAATAGTGAACATAGGCAGCTTTGTCAGCTGTGGGCAGCCCAGGAGGCCAGAAGAAAGGTGGATGCCAGGGAATTTGGGAAACTGAGGCCCAGAATTAAGTCTTGCAGTACTTTCTCTGTCCCATTTAGGGGTTAGGAGTGCTCCAAGGGAGCCAGACACCTCTTTCTCATGTCCCTTACTCAG
Seq C2 exon
TTATGTGGCAACACCCCTGGCTGCCCTCCTGAATGTTAAGGAGAAAACCCGACTGCGGGCACCTCCCAATGCCACCTTGGAACATTTCTACCAGACCAGCGGCAAGCAGCCCAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015714-Lass2:NM_029789:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF067897=UPF0258=PU(0.1=0.0)
A:
NA
C2:
PF067897=UPF0258=PU(39.8=97.5),PF0004624=Homeobox=PU(46.6=67.5)
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:
TGCTCCAGACCTTGTATGACT
R:
CTTGCCGCTGGTCTGGTAGAA
Band lengths:
278-684
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: