MmuINT0089641 @ mm10
Intron Retention
Gene
ENSMUSG00000002900 | Lamb1
Description
laminin B1 [Source:MGI Symbol;Acc:MGI:96743]
Coordinates
chr12:31318264-31320103:+
Coord C1 exon
chr12:31318264-31318633
Coord A exon
chr12:31318634-31319918
Coord C2 exon
chr12:31319919-31320103
Length
1285 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
GCTTGCTTTTCTTTCCACAGGAA
3' ss Score
11.94
Exon sequences
Seq C1 exon
CCTGTGACTGTGATCCCAGGGGCATTGAGACACCTCAGTGTGACCAGTCCACGGGCCAGTGTGTCTGTGTGGAGGGTGTAGAGGGTCCTCGCTGCGACAAGTGCACCAGAGGTTACTCGGGGGTCTTTCCTGACTGCACACCCTGCCACCAGTGCTTTGCTCTCTGGGATGCTATCATTGGTGAGCTGACCAACAGGACCCACAAATTCCTGGAGAAAGCCAAGGCTCTGAAAATCAGTGGTGTGATTGGTCCCTACCGAGAGACCGTGGACTCTGTAGAGAAGAAAGTCAATGAGATAAAAGACATCCTGGCCCAGAGCCCAGCAGCGGAACCACTGAAAAACATTGGCATTCTCTTCGAGGAGGCAGA
Seq A exon
GTAAGTAGTTAATGAGCCAAAAATCACTCACGAAGGCTTTTCAGTATTTGAAGAGCAAAGATTTCCTGGAGCGGTACGTCTGCTAGGTTTTCTAGTCTGTTACAGGCTTTGGGCCCCTTGTTTATCTACAGTGTTGTCTGTGAGCAGGGTAGATTGAGGCTCAGTGCTTGCAGCTGGACTGGACTTGAGGCAGAAGATCCATAGAGTCTCAGCTTTGCCATGTGTAAGGCTTTGAATTTGAGTGGCACATTGATTCCTGGCTCGCTCTTGCCATTGCCCTACAGCGTAATGCAAGGATAACACACTACCAGTTAAAGCCCTGAGAGTACGTCAAGTCCTAGGTTTACTTCAATCCAGTAAAAAATATTAAATGTATAGTAAAAATTGTTGATCTGTCCATGGATAGGCAGTAGGCACGTGCCTGCGATGGTGTTCACTTAGTGGAGGACAGGACAGCTTGCGAAGTCTTTTCCATCTACCGTGTGGGTTCTGGGGATCAAACGAGGTCATCATCAGACTTAGCAGCAAATAGCTTTTTACCTGCTGAGTCACCTCACAGGCTCTAGATAGATAATGATAATTTTATTACTTGTTTGTTTATTTCATTGTTTTGAAGACAGGATTTCTTTGTGTAGACCAGCCTGGCCTCAAACTCAAGAGATTCTGCCTGCCTGTGCTTCCCAAGTGCTGGGATTAAAGGCTTGTGCCACCACCCGCAGCCTGGACATTATTCTTAATTGTAATATTTTTGAGATCTGAAAAGAAATGAAAGCCTTTTTTGAATCAGTTCATTAATAAAAGTGAAACTCTGGGGAAAAACCATCACCAGGAAAGCCACTGCGTATATTCAGTGCCACCAAATCCTGTAACCCTTTTTAGTGCCTGTTCTCTGTGTTGGGTCACTCGTGGCATCCTCTCAACTTAAGGAGCATTAAATATGTGATGTGTGTCTGTATATTTGTATGTCGGGGGCTTACTGCAGCTGCCTACATTCAGAGCTGGTAGCCTGCACTCACCCTTGTTCATTTTATATCAGAGGCTTAAACTCCCCCCCCCCCCCCCCCACACACACACAAAGAGCTGAGGGTTCACTGGTATTTTTCTTCAGAGTATTTGAAGAAAAGGTGTTCGCTTCCGTTGTCTCTTTAGGAAGAAAGCTGAAACACAGGAGTATAACTGAAGTATAGTCTGAAGGTAGAGAGTGAGAGATTGTGCTAGTGGAGAACCCACAAGTAAGACTGACAGTGTGGGCCAGTTTTAGGTAAGCTTGCTTTTCTTTCCACAG
Seq C2 exon
GAAACTAACCAAAGATGTCACAGAAAAGATGGCGCAGGTAGAAGTGAAATTAACTGATACAGCTTCACAGAGTAACAGCACAGCTGGAGAGCTCGGCGCACTGCAGGCAGAAGCAGAGAGCCTTGACAAGACCGTGAAGGAGCTGGCAGAACAGCTGGAGTTTATCAAAAACTCCGATATTCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000002900:ENSMUST00000002979:24
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=0.317
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(0.1=0.0),PF0005319=Laminin_EGF=WD(100=41.1)
A:
NA
C2:
NO
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:
TGTGTCTGTGTGGAGGGTGTA
R:
TGCGCCATCTTTTCTGTGACA
Band lengths:
347-1632
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