MmuINT0089561 @ mm10
Intron Retention
Gene
ENSMUSG00000015647 | Lama5
Description
laminin, alpha 5 [Source:MGI Symbol;Acc:MGI:105382]
Coordinates
chr2:180195881-180196324:-
Coord C1 exon
chr2:180196168-180196324
Coord A exon
chr2:180196020-180196167
Coord C2 exon
chr2:180195881-180196019
Length
148 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAC
5' ss Score
5.56
3' ss Seq
GTTGTCTTGTACCACCATAGCCC
3' ss Score
5.74
Exon sequences
Seq C1 exon
GCCAGCGAAGGACCACTACTTGCCAGACCTGCACCACATGCGGCTGGAACTAGAGGAGGCGGCCACTCCCGAGGGCCACGCTGTACGCTTTGGCTTCAACCCCCTGGAGTTTGAGAACTTTAGCTGGAGAGGCTACGCACACATGATGGCTATCCAG
Seq A exon
GTGAACCATGCTGCCCCCTCCCTGGGCTTGGTGCAGAGATGGGAGCTGCTGGGTCTCTGGGGTGGCCAGCAGAGCAAGCAGCACCTGGGGATCAGGGGACTCAGGTTGACGGTCAGAGGAGTGACGCTGTTGTCTTGTACCACCATAG
Seq C2 exon
CCCAGGATTGTGGCCAGGCTGAACGTGACCTCCCCTGACCTCTTTCGGCTGGTTTTCCGATATGTCAACCGTGGATCAACCAGCGTGAATGGGCAGATCTCTGTTCGTGAAGAGGGCAAGCTTTCCAGCTGTACCAACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015647:ENSMUST00000015791:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.021
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(26.7=22.6)
A:
NA
C2:
NO
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:
CACATGCGGCTGGAACTAGAG
R:
GAAAGCTTGCCCTCTTCACGA
Band lengths:
248-396
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