MmuINT0089462 @ mm9
Intron Retention
Gene
ENSMUSG00000024421 | Lama3
Description
laminin, alpha 3 [Source:MGI Symbol;Acc:MGI:99909]
Coordinates
chr18:12649428-12650121:+
Coord C1 exon
chr18:12649428-12649572
Coord A exon
chr18:12649573-12649980
Coord C2 exon
chr18:12649981-12650121
Length
408 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CAGGACTCATTCTTCAACAGGAA
3' ss Score
6.58
Exon sequences
Seq C1 exon
GTGCAAGCCTAGAGTCACAGGGCAGCAGTGTGACAAGTGTGCTCCTGGCTTCTACCAGTTCCCTGAGTGTGTCCCCTGCAGCTGTAACAGAGATGGGACTGAGCCCAGCGTATGTGACCCAGAGACTGGGGCTTGCATGTGCAAG
Seq A exon
GTGAGACAGGTCATGTACCCAGGAGTTCTGACCTCTGATATGTTCTGTAATGTGCTAGCATTTCATACTTATTGCCTCCTTTCATAGGCATAATTGAAGGAAAGTTCTTCTTCATCCTTTGGAAAGGCCACAGACCCCTTCCCCCCTCCCTATGACAATCTGTTGATATGGACTGTTTTCTACAGTACCAAGAGACTCATAGCTTCCTTGTGATTTGTTCTTGGATAAGGACTGGGGTTATTCACCCTGCTGTAGGGCCCACTGGCTTATAGGTGGGTTCACAGCCTAGTGGGCCACCAACATGGTAGAAGCTGGGCGAGTTTCTCTCCCCCATCTGTCAGTCTTTGTAGCACTGCCTCTGTGCTTCTCAGAGCTGAAGAGTGTCTTACAGGACTCATTCTTCAACAG
Seq C2 exon
GAAAATGTAGAGGGCCCCCAATGTCAACTGTGTCGAGAAGGATCATTCTACCTGGACCCAACAAACCCAAAGGGTTGTACCAAGTGCTTCTGTTTTGGAGTGAATACTGACTGTCAGAGTTCGCATAAGCAACGAGCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024421-Lama3:NM_010680:33
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:
PF0005319=Laminin_EGF=PD(51.0=51.0),PF0005319=Laminin_EGF=PU(44.9=44.9)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(51.0=53.2)
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:
GTGCAAGCCTAGAGTCACAGG
R:
GCTCGTTGCTTATGCGAACTC
Band lengths:
282-690
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: