MmuINT0089543 @ mm9
Intron Retention
Gene
ENSMUSG00000019846 | Lama4
Description
laminin, alpha 4 [Source:MGI Symbol;Acc:MGI:109321]
Coordinates
chr10:38748428-38750390:+
Coord C1 exon
chr10:38748428-38748502
Coord A exon
chr10:38748503-38750238
Coord C2 exon
chr10:38750239-38750390
Length
1736 bp
Sequences
Splice sites
5' ss Seq
CAGGCAAGA
5' ss Score
3.01
3' ss Seq
CATTCCTATTTCATCTCCAGGCT
3' ss Score
9.02
Exon sequences
Seq C1 exon
TGTGCAACTGTGGGGGCGGCCCGTGTGACAGTGTAACCGGAGAGTGCTTGGAAGAAGGATTTGAAGTCCCTACAG
Seq A exon
GCAAGAACTGCCCAACTATAAGGAAAAGTAGCAGAACCTTAATGACTAACCAATTTCTCTAATATGCTAACAGGTGTTGCAACCCATTTGTAGTTTTTTTTTTTTTTAAATCGAAAATGTGGAAGAAAAGAACTGATTCCCACAAGATACCCTCTGACATCCACACTCACATTTGCGCACACACACACACACATCACAATAAGTAGTAAATGTATGAGTGTGATATCACTTTCCCTGAAAGGGTTTCACTCCCACCCCTGGTTTAGCAGCTGGTATTTGCTCCAGGGTAACGGACCTTGTGCAAAGGTCCCTGGTGGCCTCCATCTCAGTCAGCAGTGAGGCAGTTTTTGCGGACCTCACTCTGAGACTTTAGACATCTTACTTACCTAGTCTTCACACTCAGCTCTCAGGACAGAGCCCTGTCTACGTTGGCTGACTGGTGCTACCCGGGCAGCTGTAGAAACTGAAAAGCCAGGAGACTTAAGCAGCTCTTCCCGACACACCCAAATGTGAAGACTGACCAGAAGTAAACTGACAAGGAGTTACAAAGTAGAGCTGCCTTCTCTTTTGCTTAAATTGCTCTGTCACTCAAGAGCAACGAAAATTTTTTGTCTCAAAGAGTATTTGAACATCATGCATCCCTTCCTCCAAGGAAAAGTATATCGGTCCCAAAAAAGTCCTTGTGGGTAGAAGATTATAAAACTGCCAGTTTATCATCTCTTAGAAGATGCCCGAGATGTGAGACACAGCAGGGAAAAGCCTGCAGTTATCAACTACAGCATCCTGGACTAGCTCCACTTAAAGGCGGCCAGATGCCTACATAGCCTTAAACATTTTTCTTCAGCAGCCTGAAGTGTAGTCTGGGGACTCATTTTCTAAGGGAGCTTAAAGGTAGTGCTATGTTAATAACAAATTAACAAATGAGCATGCATTAACCCTTTAGTGTCTGACAACTCTGCAGGAAATAGCAGAGCCTGTGGGAAGGAGTTTGGGAATCGGCAAGGTGCAGAGAGGCCAGGATGGGGCTCAAGGCTTGGTGTGTGTTCTTTTTAATTATGTCCATGGAGGGCAGCTGGGTTCCGGGTGGGGCTCACAGTGTGAAAGGTGAGGAGAGAGAAGCTGGGGCTTGTCTCTTGAGCCTGTCCAGGTTTAGTTTCAGCTTTAGCTCCTACCTCAGAGACCAAGTCATGACATTAGCCAACAAGTGTACCCTACAGTCCTGCTCTGAGGACTTGTTCATCTAGACACAGGGTCGTGGTGGGGGGCATGGAGAGGAGCCAGGCCCTCCCTGGGGGAGGCAAAGGCAGGTGCAGCATTCCTGGACTGACTGAGAGAAGCTGATGAGAAAAGAATGATGCTTGGCCCCCAGCCTGCTCTACCAGCTGCCACCAAGCAAAGACAGGAAGCTGACAGGATCAGAATCTGGGGGGTAAGGGGACCATGAATAATAGGAAAAGTGGTAAGGGCTTCTTCTCCACCTATCCTATAATAGTCCTTTCTGTTAACAATTAGTGTTCTTATTAACCTGCTGTCTCAATGTCTGGTTCTCATTATGTTAAGTGGGACTCCTGCCCGATGTATGGCTTGGTTTGGTAAAGACAGGTTCTATGTGGCCGTATCAATTTCTTGGGAAATAAAAATAAACATGGTACTAACCAAGGGGGTCTATATTAAAGCCATATGAATCCAGGCTGCCTTTTGGCTCTGCAGAAATGACATTCCTATTTCATCTCCAG
Seq C2 exon
GCTGTGATAAGTGCGTCTGGGACTTGACCGATGACCTGCGATTAGCAGCGCTCTCCATCGAAGAGAGCAAATCCGGGCTGCTGAGCGTGTCCTCTGGCGCTGCGGCGCATAGACACGTGACCGACATGAACTCTACCATCCACCTCCTCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000019846-Lama4:NM_010681:6
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:
NO
A:
NA
C2:
PF060089=Laminin_I=PU(11.0=56.9)
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:
CGTGTGACAGTGTAACCGGAG
R:
TCTGAGGAGGTGGATGGTAGAG
Band lengths:
206-1942
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: