MmuINT0089536 @ mm9
Intron Retention
Gene
ENSMUSG00000019846 | Lama4
Description
laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321]
Coordinates
chr10:38816889-38818292:+
Coord C1 exon
chr10:38816889-38817044
Coord A exon
chr10:38817045-38818132
Coord C2 exon
chr10:38818133-38818292
Length
1088 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATC
5' ss Score
6.99
3' ss Seq
GTAACTTCTTCTTCTTCCAGATT
3' ss Score
9.48
Exon sequences
Seq C1 exon
GTGATATTTATTCGGGAAAAGAGCAGTGGTCGACTGGTCATTGATGGTCTACGAGTCCTAGAAGAAAGGCTTCCCCCTAGTGGCGCTGCCTGGAAAATCAAGGGTCCCATTTATCTGGGAGGAGTGGCTCCCGGAAGAGCCGTGAAAAATGTCCAG
Seq A exon
GTAATCCAGCTATGGCAAGGCTGAGCCACTGACCCCATGAACCGGAAGCACACTGATTCCAGGTCCTCATTTTACTGGGTAGGAACCTAGTAAAAGTGAACCAGTTCTATTGGGGAAAAAATAAAAACCATTCTAGGCTGTACTGTGGGATTCCTGCCTGCCCTGGAGCATTTTGACTTTTAAAATAGAAACGAGATGAAAAAAGTTTAATAGTATAAACTGTCCTAAAACTTATGTCTCCAGGGGGCTTTATTAGTTCTACAAGTACCTATAATTTTAATGTAAAGCTACAGTAAGACCAGATAACAAGTCATTCTACTATGTTACTGAATGCAAAACAAACAAACAAAAATAAAAAAAACTTCAGCTCATTTAAATTCAGTTCCATTTTTTTCTCTTTCTCACAATTTCTCAATATGCACAGATGCACATATAAGTGCAATTCTTCAATTGGGAATATAAGAAACATTTTTATAAATCAAACTATAAGTAATACTTGTTTTTAAAGTGTTTCTCAGTGAGAGGAAAGTATGGAAAAACTTAATTTATCTTAAACACAAACGTAGATTTGATTTTATCACAGTGTCAGTACATTGTTAAGATCCACTGGCAGATAAGTAGGAAAGGGCGTTTACATTATAATTAGACTTGAAATAAACAGCCAATTCTGTGGCAGGCGTTTTCACTGTTCTCAAGTGTGGTATAAAACTAGTTGTCTACAGTGATCCAAGTGTCATGTCCCATGGTATGATTAAGTTTGCAACTGCATTACAAGCTAATGAAGCCAGATCGGCTAGCTGCCTCCCGTTGGCAAAGTACTTTCATCCACATCCGCGATCTTGGACCCAGCCTCATTCCTGAAGGAAAATGAAAGATAGAAAACCGCAGTTTTCAACTGGAAAACCGCAGTTGCAACTTATTAATATAAACTCCTAGCTTTGATGAATTAGTTAAAAGTAATTGCCAGGAAGGAGCAATATTGATCATTCAGAAGCTAAAATGAACAAGGGCTAACTCACTTGTTCACTTTCCCATGGTGCATCTGGGTGCTGGGCAAGGGGATTCTAAGTAACTTCTTCTTCTTCCAG
Seq C2 exon
ATTACCTCCGTCTACAGCTTCAGTGGCTGCCTTGGCAATCTCCAGCTCAATGGTGCCTCCATCACCTCCGCTTCTCAAACGTTTAGCGTGACCCCTTGCTTTGAAGGGCCAATGGAAACAGGAACTTATTTTTCCACAGAAGGCGGCTATGTGGTTCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000019846-Lama4:NM_010681:33
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:
PF0221019=Laminin_G_2=FE(39.8=100)
A:
NA
C2:
PF0221019=Laminin_G_2=PD(14.1=33.3)
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:
TTTATTCGGGAAAAGAGCAGTGGT
R:
CTAGAACCACATAGCCGCCTT
Band lengths:
310-1398
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: