MmuINT0012837 @ mm10
Intron Retention
Gene
ENSMUSG00000041936 | Agrn
Description
agrin [Source:MGI Symbol;Acc:MGI:87961]
Coordinates
chr4:156170066-156170411:-
Coord C1 exon
chr4:156170315-156170411
Coord A exon
chr4:156170231-156170314
Coord C2 exon
chr4:156170066-156170230
Length
84 bp
Sequences
Splice sites
5' ss Seq
AGGGTTAGT
5' ss Score
5.02
3' ss Seq
ACAACTCCACATGACCCCAGGGA
3' ss Score
3.83
Exon sequences
Seq C1 exon
TCCTGGAGAATGCTGGCTCCCGGCCCTTCCTGGCTGACTTTAATGGCTTCTCCTACCTGGAACTGAAAGGCTTGCACACCTTCGAGAGAGACCTAGG
Seq A exon
GTTAGTGGGGAAGGAGGGCTAAGGGAAGGGAGCTAACCTGACGAGGAGACGGTGACACACTCCCACAACTCCACATGACCCCAG
Seq C2 exon
GGAGAAGATGGCGCTGGAGATGGTGTTCTTGGCTCGTGGGCCCAGTGGCTTACTCCTCTACAATGGGCAGAAGACGGATGGCAAGGGGGACTTTGTATCCCTGGCCCTGCATAACCGGCACCTAGAGTTCCGCTATGACCTTGGCAAGGGGGCTGCAATCATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041936:ENSMUST00000105574:27
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005418=Laminin_G_1=PU(34.8=82.1)
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:
GCTTGCACACCTTCGAGAGAG
R:
TTGCCAAGGTCATAGCGGAAC
Band lengths:
175-259
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