MmuINT0089548 @ mm10
Intron Retention
Gene
ENSMUSG00000015647 | Lama5
Description
laminin, alpha 5 [Source:MGI Symbol;Acc:MGI:105382]
Coordinates
chr2:180201458-180201855:-
Coord C1 exon
chr2:180201721-180201855
Coord A exon
chr2:180201521-180201720
Coord C2 exon
chr2:180201458-180201520
Length
200 bp
Sequences
Splice sites
5' ss Seq
ACCGTGAGG
5' ss Score
4.23
3' ss Seq
TATGCTGTCTCCTCCCTCAGCTC
3' ss Score
9.44
Exon sequences
Seq C1 exon
CCTGCGACTGTGAGTCAGACTTCACGGATGGGACCTGTGAAGACTTGACGGGCCGCTGTTACTGCAGGCCGAACTTCACAGGAGAGCTATGTGCTGCCTGCGCTGAGGGCTACACGGACTTCCCACACTGCTACC
Seq A exon
GTGAGGGCCAGCAAGGAACTCGGGGTGGGGGTGGGGCTGTTTGGGAAGGCCCAGGGTCACAGTCTGACGGGATCAAAGGGCCTAGGAAGGGTGGAAGAAGACCCAGGGAGTCGCCCAGAGCCCCTGGGTGGTCTGTGGTACTGGAGCCAGAGAGCCTGCTCCACAGACCTGGTGGACAAGTATGCTGTCTCCTCCCTCAG
Seq C2 exon
CTCTGCCTTCATTTCCCCACAATGACACGAGAGAACAGGTGCTTCCCGCTGGACAAATCGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015647:ENSMUST00000015791:10
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=PU(91.7=95.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(6.2=13.6)
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:
ACTGTGAGTCAGACTTCACGGA
R:
TCACGATTTGTCCAGCGGGA
Band lengths:
192-392
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