MmuINT0065279 @ mm10
Intron Retention
Gene
ENSMUSG00000026193 | Fn1
Description
fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566]
Coordinates
chr1:71641952-71643151:-
Coord C1 exon
chr1:71642960-71643151
Coord A exon
chr1:71642132-71642959
Coord C2 exon
chr1:71641952-71642131
Length
828 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
ACTCTTGGTTATGCTTGTAGCCG
3' ss Score
4.25
Exon sequences
Seq C1 exon
GATCTGGCTCCTTCACTGATGTCCGAACAGCTATTTACCAACCGCAGACTCACCCCCAGCCCGCTCCCTACGGCCACTGTGTCACCGACAGTGGTGTGGTCTACTCTGTGGGAATGCAGTGGCTGAAGTCGCAAGGAAACAAGCAAATGCTGTGCACGTGCCTGGGCAATGGCGTCAGCTGCCAGGAGACAG
Seq A exon
GTAGGCACCATCTGCCCACGGATGCCAGAGGACCTACATTCAGTGTCTGCAGTATCTTAGCTGTTCGTAAAAAAAAATGTAAAACCATAAATCCAGAAAAGTTTATAATCCTGTGATAAAAATCATAGTAGCTGACATTTTCTTCTCTGGTCTTTTTTTTTTTTTTTGGTTTTTTGAGACAGGGTTTCTCTGTGTATCCCTGGCTGTGGCCTTGAACTCAGAAATCCCCCTGCCTCTGCTTCCTGAATGCTGGGATTAAAGGCGTGTGCCACCACGCCCGGCTCTTCTCTAGTATTATAACTTGTATATTTTCTTCCTATCATGAGGATCAAACTGCTTTGTAGTATCTGTATTTGCCGAAAGGGATGCTGCAAGAACACCATTTTTTTCCTGTTTGTTTTTGTTTTTTCTCAACTAGCCAATAATCTGTACTCTGAGTTCAATTTGGAATTATAGATGTCTTTTAGCAGCACATGGCCTCTTCTGGGTCAAACATGCTCTCTTTTATAATTGTTTTTCTAGAGCAGCCATATATACTGTTTCTTCTGAGAATGTAAGCAAGCATGTATCGCTCTGTGCCGTCTTCAAATCATAATAATTTGTATTAATAAAGCTTTACAAGTGGGGAAACTGAGTCACGGTAGCAGAAGTGTCTCCCAAAGACATTAAAAGGAGAACTCTGGCTCACCCTTAACCAGCTGACTAGACTTTTCATCTTGGCCCTTTAGTAGCACAGTTTCCATTTAAATTAGAAATTTGTCACCACTGGGGTCAGAGGTGAGGGTGGGAAACAACTGTACTGACTGAGACTCTTGGTTATGCTTGTAG
Seq C2 exon
CCGTGACCCAGACTTATGGTGGCAATTCAAACGGGGAGCCCTGTGTCCTCCCGTTCACCTACAACGGTAGGACCTTCTATTCCTGCACCACCGAAGGGCGGCAAGACGGACATCTGTGGTGTAGCACAACTTCCAATTACGAACAAGACCAGAAGTATTCCTTCTGCACAGACCATGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026193:ENSMUST00000055226:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0003913=fn1=WD(100=53.8)
A:
NA
C2:
PF0004014=fn2=WD(100=68.9)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGAACAGCTATTTACCAACCGC
R:
GCATGGTCTGTGCAGAAGGAA
Band lengths:
347-1175
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