MmuINT0089476 @ mm9
Intron Retention
Gene
ENSMUSG00000024421 | Lama3
Description
laminin, alpha 3 [Source:MGI Symbol;Acc:MGI:99909]
Coordinates
chr18:12683235-12683686:+
Coord C1 exon
chr18:12683235-12683346
Coord A exon
chr18:12683347-12683518
Coord C2 exon
chr18:12683519-12683686
Length
172 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGA
5' ss Score
5.96
3' ss Seq
AGCTCCTTGATGTTTTCCAGTTC
3' ss Score
6.28
Exon sequences
Seq C1 exon
GCACAGGTCAATTCCAGAAAAGCACAAACATTATATAACAACATTGATCAGACAATCCAAAGTGCCAAAGAACTGGACATGAAGATTAAAAACATCGTTCAGAATGTGCACA
Seq A exon
GTAAGAAAAGTTACCCAGTCCAATTAAAACCTTTATTGCATAACCTTTGTTAGATATTTTTGAGAGCTCAGCACTATGAAAGAAGATCCCCCGGTGATACTTAAAAGATGAACAGGGTTCTCCACCAAGCTTCCAGAGCACTCGAGTTAATAAGCTCCTTGATGTTTTCCAG
Seq C2 exon
TTCTCCTGAAGCAGATGGCGAGGCCAGGTGGAGAAGGCACGGACTTGCCAGTGGGTGACTGGTCCAGGGAGCTGGCCGAAGCTCAACGCATGATGCGAGACCTGCGAAGCCGAGACTTTAAAAAGCACCTCCAAGAAGCAGAGGCCGAGAAAATGGAAGCCCAGCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024421-Lama3:NM_010680:46
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.079 A=NA C2=0.491
Domain overlap (PFAM):
C1:
PF060089=Laminin_I=FE(13.9=100)
A:
NA
C2:
PF060089=Laminin_I=FE(21.0=100)
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:
GCACAGGTCAATTCCAGAAAAGC
R:
CTCTGCTTCTTGGAGGTGCTT
Band lengths:
255-427
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: