MmuINT0089509 @ mm10
Intron Retention
Gene
ENSMUSG00000024421 | Lama3
Description
laminin, alpha 3 [Source:MGI Symbol;Acc:MGI:99909]
Coordinates
chr18:12419166-12419928:+
Coord C1 exon
chr18:12419166-12419256
Coord A exon
chr18:12419257-12419796
Coord C2 exon
chr18:12419797-12419928
Length
540 bp
Sequences
Splice sites
5' ss Seq
TCCGTAAGT
5' ss Score
10.27
3' ss Seq
TTTTTGGTGTTTCCTCTTAGCTT
3' ss Score
7.69
Exon sequences
Seq C1 exon
CACAACACTGCAGGCGTGAACTGTGAAAAGTGTGCGAAGGGTTACTTCCGGCCCCATGGAGTTCCGGTGGATGCACTGCATGGATGCATCC
Seq A exon
GTAAGTTTCATGTCAATTTTGTGAGCATGACAGGCTGTGTGTACCACCCTGAGGGCGTCATAGGCTTGGGACCAGCTGACGGTCTTGGTTCCCTTGCCTACCTGGTGTTGGCTCTGCTTCTCCCTAGTTGTCTCAACTCAGACAGCTCAATGTTTTCTCTGAGCCCCAGAATGCTTGTATGTAAATGATAATGATAATAAATATTATTTCATAATTATAGGTGAAACACTATCAAATGTATCTAGGCAAGCACTTAATTCATTGGGTCGATCACTATTAAATCTGCAATTAATATTGCTTCTTTCATTTTCTACTGGTTTGATGTGTTTCTATGATCTCCAATAATTCCAACTTTGTCATAATTAGAATCAAAACAGTATAGTATTAAGTCCACAAAGAATTAATAATATTCATAGTGTTTAGCTATAGCTTACTACGCACGAGAGATAGCCTGAGCCAATGGGCAATGCTAAGAAGTTTAGGGGAAAGTCTGCTTTTGGAAGTACAGTGAAGAACTGGTTTTTTGGTGTTTCCTCTTAG
Seq C2 exon
CTTGCAGCTGTGACCCAGAACGCGCAGATGACTGTGACCAGGGCTCAGGCCACTGCCATTGTAAGCCAAATTTCTCCGGAGACTACTGTGAGACGTGTGCAGATGGGTACTATAATTTTCCATTTTGCTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024421:ENSMUST00000092070:9
Average complexity
IR
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(41.2=90.3)
A:
NA
C2:
PF0005319=Laminin_EGF=WD(100=97.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
CACAACACTGCAGGCGTGAA
R:
ATGGAAAATTATAGTACCCATCTGCA
Band lengths:
214-754
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