MmuINT0089582 @ mm9
Intron Retention
Gene
ENSMUSG00000015647 | Lama5
Description
laminin, alpha 5 [Source:MGI Symbol;Acc:MGI:105382]
Coordinates
chr2:179923272-179924268:-
Coord C1 exon
chr2:179924038-179924268
Coord A exon
chr2:179923386-179924037
Coord C2 exon
chr2:179923272-179923385
Length
652 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
CCCTACCTGCCTTTCTCCAGGAA
3' ss Score
10.32
Exon sequences
Seq C1 exon
GGGAACTTCCGGCACTTGGAGACTCACAACCCCGTGTCCCGAGAAGAACTCATGATGGTGCTGGCCGGCCTGGAGCAGCTGCAGATCCGTGCTCTCTTCTCGCAGACCTCTTCCAGTGTCTCCTTGCGTAGAGTGGTACTGGAGGTGGCTAGCGAGGCTGGTAGGGGGCCTCCAGCCAGCAATGTGGAACTGTGTATGTGCCCTGCCAACTACCGTGGGGACTCGTGCCAG
Seq A exon
GTAAAGGGGTGAGGGTGGGCGCTTAGCCATGAAGGTGCTCCCCGCGGGTCCTTCCCCAAGCATACTCTGCCAGCATCTGCTTTCTACCCTGTCCCATGTCTGCCCCTGCCCGAGTGTCTTCCTCTCTGTCCCTCTCAGCCTGCATGCTTGCTCAGGTGTCTGCTTATCCTCACCTGCTGTCCCAGCATTCACCACTGCCTACCGCTCCATACACACAGCTGCCGTGACCTGTCCATTGCTCACCCAGGACCCACACAGTCAGCATCCCTGATCCACCCTGATTCCCACTCTCTCCTCCCTCACCTGGGGATCTGGGTAGTCTAGCATGATACCCAGGGAAGGTTTATGTCTGACCACCACTAGAAAAAGATGTTCAGGGTAGAAAGAAGGTGGCCCTGGTGGGTCGCTAGTCCCACAGGCTGGTCATTCCTGAGCCGTGATATCCACATCTGGCACAGTGTCCATAAGTCTAGAAGCCCAACAGACATGGCCAGCAGTTCTGGTGTCCAACTCCCTATGATCCAGTGTATGCTGTCCCTGTAGCCTCTGTAGTGCGTGAAGGTCCCAGAGGCTGATGGGAGAGCAGCCTCTCTAGTCTGCCCAGCCGTGGGGCTGGCATCCAGTCACTAATGCCCTACCTGCCTTTCTCCAG
Seq C2 exon
GAATGTGCCCCTGGCTATTACCGGGACACCAAGGGTCTCTTCCTAGGCCGATGTGTCCCCTGTCAGTGCCATGGCCATTCAGATCGCTGCCTTCCTGGCTCTGGCATTTGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015647-Lama5:NM_001081171:41
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:
PF0005213=Laminin_B=PD(45.3=80.5),PF0005319=Laminin_EGF=PU(48.6=23.4)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(45.9=44.7),PF0005319=Laminin_EGF=PU(35.4=44.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAACTTCCGGCACTTGGAG
R:
CACAAATGCCAGAGCCAGGAA
Band lengths:
342-994
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: