MmuINT0089440 @ mm10
Intron Retention
Gene
ENSMUSG00000024421 | Lama3
Description
laminin, alpha 3 [Source:MGI Symbol;Acc:MGI:99909]
Coordinates
chr18:12439334-12441141:+
Coord C1 exon
chr18:12439334-12439471
Coord A exon
chr18:12439472-12441094
Coord C2 exon
chr18:12441095-12441141
Length
1623 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CGTCTCTGAATTATATGCAGGGT
3' ss Score
6.28
Exon sequences
Seq C1 exon
CTTGCCAGTGTTCGACGATTGGATCCTATCCAGTGCCCTGTGACCCGGGGAATGGCCAGTGTGACTGCCTGCCTGGAATTACCGGGAGGCAGTGTGACAGGTGTCTCTCGGGAGCCTATGACTTTCCATACTGCCAAG
Seq A exon
GTAAGGAAGCCGGCAGCATGTTGGAGGCTCGGTCCTCATCTGAGTGGGTGCAGCTGACCTCTTGGAGAAGCCTGGTGAGTCTTCTCTACATTGGCTCAAGCCCCCTAAGTATTTGGTCCAGTCTTCCCTATGCCAGTGTCACTGGAAGCATGTGCATCATGGCTCGACCCCAGAGACAGTCGGTGCCTGATGAGAACAACTTAAATACCCGTTCATAAACAATCTGGGTTTCTCAGCCCTCTGCATCAGCGTAGTCACATGACCCCACAAATCTGCCCTTGCATTGTTTGACACCCCACCGAGACCCTATGTACCAAGGCATCATGCCTCTCTCCCTAGTGACTCTTAGTGCTGATATGGGCTGCATAAGATCTTTGCTGTAGGCTAAGAGGGACCAGGGCTGTGTTCTGCCTCTTCTCCCAACACAGAAACGAGCTACCTGCATTTCCCCAAGCTCTTTGATGTGGCAGACCCAGACCCGCCAATAATTCTGGCCTGGTGATTTCAGAGTTCTCTTGTGCTATGGAGCAGGGCAGTTTGTAGACTGACCCAGACTTTCCATCAGAAAAATGTGGTTTTTGTAGGAACCCTCCTGGTTCCTGGGGACACTGAGGGTGAAGCATCCAGAGCTGGGTGGGACTATGTAGAAGAGAGGGTCACATTTCCCAGAACTTTCCTAATCAGAATTGTCCAGACCAGGGCAGAAAGTGCAGTCAGCAATAACAGGGCTTGCCCTGAGAAGGCCTGTATGTCCTTGTGTGGTCATCAGGCCTGTGGGTGATGTGGTAGAGTAGCCAGAACTATACCCGAGCTGGAGAGTGACACAGTCCATGCTGGGAGGAGCCCAGGACAGGCATGGTCAGTACAGAAGACAAAGGAGAGAAAGTGAGGTGTGGGCTGCCAGAGAAGGAGGAGCAGAGAGGAGGAAGAGGAGCAGGTCTTCATGAGAACGGAGACAAACTTACAAAGAGGAAACACTGGGGAAAAGCAAAAGGGCAATTCGTGAGGATATACAATCCTGTTGTGGATATGGTCCAATGGCGAAAACCAGCCATAGACGCAGTGTACTACCAAACAGTGTAATCAAGACATTGCAAGTGCTCAGCTATAGCCTCTGCAGGCGAAGACAGGAAAGCACACCAGCTTTGTCACCAAGAACCTCAGTACACATGGGGACAGGGAGAATTATAGTGCAATATCGCCCTCTGCTGGACAATTCTAAAGCTGCTCAAAGTTTCAGTGTAACCATCACCCATTAGAAAGGAGGTTTTGCAGAGAAGGATCTGGGAAGAGTTGAGGGAGGGAAGAGAAAGTGATCAAAATATATTACATGTAATTCTCAAAGTCAAGTTAAAATATATATTAAAACTAGAGACTAGCAAGCATTAAACCCAGAAAGGAAGTTGTGTTCCTAGGCAGGGCAGAGTTACTGAGTGACGGATGAGTCAGAGCAGATCAAGCATAAAGTTTGTTCTCTTGGCATGTCTTAGTGTAGCTACACATGGTCTTTGTCACGCATCTATAAAAGCATACATGTAGGTGCACTTACAAGAAAGAAAATTTAAAAATCTGAAGCACCTAAATGATCAGCCAGGTGTTGTAACGTCTCTGAATTATATGCAG
Seq C2 exon
GGTCCGGCAGTGTTTGCCATCCAGCTGGGACCCTTGACTCCAGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024421:ENSMUST00000092070:13
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(0.1=0.0),PF0005319=Laminin_EGF=PU(88.2=95.7),PF0005319=Laminin_EGF=PU(5.9=6.4)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(9.8=31.2),PF0005319=Laminin_EGF=FE(29.4=100)
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:
GCCAGTGTTCGACGATTGGAT
R:
CAGGCTGGAGTCAAGGGTCC
Band lengths:
182-1805
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