MmuINT0065269 @ mm10
Intron Retention
Gene
ENSMUSG00000026193 | Fn1
Description
fibronectin 1 [Source:MGI Symbol;Acc:MGI:95566]
Coordinates
chr1:71597281-71598463:-
Coord C1 exon
chr1:71598374-71598463
Coord A exon
chr1:71597748-71598373
Coord C2 exon
chr1:71597281-71597747
Length
626 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
CTCTAACCTCTCTTGGCTAGATG
3' ss Score
5.45
Exon sequences
Seq C1 exon
GTCTGGAGCCAGGAACCGAGTACACCATCTACGTCATTGCCCTGAAGAACAATCAGAAGAGTGAGCCCCTGATTGGGAGGAAGAAGACAG
Seq A exon
GTAAAGACTCATAACCAGTGGTTGCTTTGCAGGGTGAAGTCTCTACATTTCCACACATCACACATCTCTCACGGATTTTTTTTATTTCCCTAGCAGAGTGGCTTATATATTTTACTCTTTGACAGGAATCACCTAACATGCTCTAAAAATGTCTGATTTATTTCTTTTTCTACAACCTTAAGCTTCGTTTACCTTGCAGAGATTCAAACTAGATAGTTTGAATTGGAAGGGGGGGGAAGCTTTATAATGGTGGGAGTAAAACCTTTCTGATTTGGGTCGATTTATTTATTATTTGATTTCTGAACTTCAAACACTTCAGTTCGTTGCAAAGCCTTAATTGGAGCAGAGATGGCTTTCTGTGGGGCTCAGCGGTTCAAAGCTTTGTCTGTATGAGAATTCATACTAACTTTTTTTTTTTTCTGTCTGAACTATAAAGAAATCTGTGAGAAAAAAAAAATCACGATTTCTTTCTCTAAGAGTGTTTTGTGATCTGAGAACCGCTGGTTGTGTGGGAGCTCTGATCGGGTTGATAAACAGTTGTTGCCTGGGTTGACAGTGATTGGTTGCTTCTTCTTCGAGCTTAACTTTTGCGCTTTGCTTTTTTGGCTCTAACCTCTCTTGGCTAG
Seq C2 exon
ATGAGCTTCCCCAACTGGTTACCCTTCCACACCCCAATCTTCATGGACCAGAGATCTTGGATGTTCCCTCCACAGTTCAAAAGACCCCCTTCATCACCAACCCTGGGTATGACACCGAAAATGGTATTCAGCTTCCTGGCACAACCCACCAGCAACCCAGTGTTGGGCAACAAATGATCTTTGAGGAACATGGCTTTAGGCGGACAACGCCACCCACTGCGGCCACCCCCGTCAGGCTTAGGCCAAGACCATACCTGCCGAATGTAGATGAGGAGGTCCAAATCGGTCATGTTCCCAGGGGAGACGTAGACTACCACCTCTATCCTCATGTTCCGGGCCTCAATCCAAATGCCTCTACAGGACAGGAAGCTCTCTCTCAGACAACCATCTCTTGGACGCCGTTCCAGGAGAGTTCTGAGTACATCATTTCATGCCAACCAGTTGGCACCGACGAAGAGCCCTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026193:ENSMUST00000055226:39
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.351 A=NA C2=0.801
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(27.2=71.0)
A:
NA
C2:
PF0004116=fn3=PU(51.4=23.7)
Main Inclusion Isoform:
NA
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:
GAAGAGTGAGCCCCTGATTGG
R:
GGTGGTAGTCTACGTCTCCCC
Band lengths:
353-979
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