MmuINT0089625 @ mm10
Intron Retention
Gene
ENSMUSG00000002900 | Lamb1
Description
laminin B1 [Source:MGI Symbol;Acc:MGI:96743]
Coordinates
chr12:31265293-31266866:+
Coord C1 exon
chr12:31265293-31265601
Coord A exon
chr12:31265602-31266690
Coord C2 exon
chr12:31266691-31266866
Length
1089 bp
Sequences
Splice sites
5' ss Seq
TAGGTAACT
5' ss Score
6.43
3' ss Seq
GTTGCTTTTCTTTTCTGTAGCCC
3' ss Score
8.35
Exon sequences
Seq C1 exon
CTTCTTTGGGCCGGTGGGCTGCCAGGAGCGGGTTGAGCGCTCGCCCAGCCGGGTGAGGAGAACAAAGTAGTTAAGCGACTTGACCCCCTTCCTGGGCCCAGCCCCCGCTTCCGTGGGAGCGGCAGGAAATGGAAGGGCCCCTCTCCTCTCTCCCAACATTTGCCTTTTCTCCCCGCTACCTCTCCAGAAAGGAAGACCCGAAGAAAAGACAGGCAGCTTGCCTGCTGCGTCCTCCTTCCCGTGCCGCGTCCCCTCGTCTGCGAGGACTGGACATGGGGCTGCTCCAGGTGTTCGCCTTTGGTGTCCTAG
Seq A exon
GTAACTCAGTAAGGGTTGGGGGGAGGGGTGTGCTCCGGCATTAGGGAAGAAAACCCCCAAACCGGTTTGCCCCCGCTTTGAAGGCAGTTTTGGGGGATCGGGGGAGAGAGAGTGGTTGGAAATGACGCCGTGAGATCGCCACCGCTCTCGCTTCGGTGGTGGCCAGGGACCGCGCACGCGGAGCTCCGCGGACCCGCATCCACTGGGTTCTGCGCACAGAGCTCGCGCTCCTGCAGGTTTCCGAGGTGATCGCTCCAGGGCTTTGCACCTTTTACCAGTTAAACGCTGTTTCCCCACTGCGGAAGGCAGGCTCCCTGCTGTGGCTGGGCAGACTGCGGAGGGTCCTGGAAAAACCAATTACGCACAAAAGTGTCGGGGCCCAGAGCAGGCTTCGACTTGGGAACAGATTGGAGCCATGTGGCTTTAATTAACCATCCTTGTTTGTCTCGGGGTGGCACCATGAACAGTTGGGCCGGGTGCTTTGCTGGAATGGCGAAGCGTTGAAGCCACTACAGAGACACACCAGTCGTCTCTAGCTCAGGGCTTCTGTGGCAAACGCGGTGCCTCACCCGGCGCAATCGCCGGTGACCCTGGCGCGTGCACGCGGACATATTTTTGTGCCCCCCCCCCGCCCCCAGACTAACCACACTCACACCGAGGATGCGCGCACTGCCATGTGCACGCGGGTTTTCATTAGCGGGTGTGCAGCGCTTGGCAGGGTCAACCTCACTGCGCCCTGGTCCAGGCACTTCGAAGTGACCGGATCACTCTGTCCACCTTTCATAGAGGGGTAGATCAGAGTAGACAAAAAAGTCAGTTGTATTTTCTGGGTGCTGCGCTCAGCTGACTGCTAGTCAAACCTAATGACGATTCTGAGTCTTTTTTTTTTCTTTCATCCTTCTGTCTTTTCCTTGTCCCAGCTTTCCAGGCCTTTTCTGCGCCTATCTCTCCACCGTGTTTTTTCTATGTAGTCTCCTTTCTTTTTAATCCTCTCTGTCTGCCCCTCCTGCTGTTTTCTTTTGCCCTGGCTTGTCGGTTGCTTTTTTTTTTTTTCTTTCTTCCTAACCTTGTTGCTTTTCTTTTCTGTAG
Seq C2 exon
CCCTATGGGGCACCCGAGTGTGCGCTCAGGAACCGGAGTTCAGCTATGGCTGCGCAGAAGGCAGCTGCTACCCTGCCACTGGCGACCTTCTCATCGGCCGAGCGCAAAAGCTCTCCGTGACTTCGACATGTGGACTGCACAAACCAGAGCCCTACTGTATTGTTAGCCACCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000002900:ENSMUST00000002979:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.003
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005512=Laminin_N=PU(15.3=61.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCGGCAGGAAATGGAAGG
R:
GTAGGGCTCTGGTTTGTGCAG
Band lengths:
348-1437
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