MmuINT0089588 @ mm10
Intron Retention
Gene
ENSMUSG00000015647 | Lama5
Description
laminin, alpha 5 [Source:MGI Symbol;Acc:MGI:105382]
Coordinates
chr2:180186562-180186981:-
Coord C1 exon
chr2:180186801-180186981
Coord A exon
chr2:180186712-180186800
Coord C2 exon
chr2:180186562-180186711
Length
89 bp
Sequences
Splice sites
5' ss Seq
GGCGTGAGT
5' ss Score
7
3' ss Seq
GCCTACCCCTCTTCCTGCAGGCT
3' ss Score
10.72
Exon sequences
Seq C1 exon
GAAGGATACTTCGGTTTTGAGCAATGCCAGGGCTGCCGCCCTTGTGCCTGTGGACCAGCTGCCAAGGGCTCCGAGTGCCACCCTCAGAGCGGTCAGTGTCACTGCCAGCCAGGGACCACAGGACCCCAGTGCCTCGAGTGCGCCCCTGGCTACTGGGGCCTCCCAGAGAAGGGCTGCAGGC
Seq A exon
GTGAGTACAGGACTGTGGGAAGGCAGGGTGGAGAGAGGCAGGCATCCCTGAGCGCCTCCAGTCACATCTGCCTACCCCTCTTCCTGCAG
Seq C2 exon
GCTGCCAGTGTCCCCGAGGCCACTGTGACCCACACACGGGCCACTGCACCTGTCCCCCGGGGCTCAGCGGGGAACGCTGTGACACCTGCAGCCAGCAGCACCAGGTGCCTGTACCGGGCAAGCCTGGGGGCCATGGCATACACTGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015647:ENSMUST00000015791:47
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=0.020
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(24.4=18.0),PF0005319=Laminin_EGF=PU(92.0=75.4)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(6.0=5.9)
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:
CCCAGAGAAGGGCTGCAGG
R:
TTCACAGTGTATGCCATGGCC
Band lengths:
169-258
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