MmuINT0012827 @ mm9
Intron Retention
Gene
ENSMUSG00000041936 | Agrn
Description
agrin [Source:MGI Symbol;Acc:MGI:87961]
Coordinates
chr4:155547112-155547789:-
Coord C1 exon
chr4:155547652-155547789
Coord A exon
chr4:155547240-155547651
Coord C2 exon
chr4:155547112-155547239
Length
412 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TCACTGCCCCTCCCCCACAGCTA
3' ss Score
10.37
Exon sequences
Seq C1 exon
GACTTGAGCCCCCGGTGGGCAGCGTTGTGGTGACCCACGGGCCACCCATCGAGAGGGCTTCCTGTTACAACTCACCTTTGGGCTGCTGCTCAGATGGCAAGACACCCTCACTGGACTCAGAAGGCTCCAACTGTCCAG
Seq A exon
GTGAGTGAACAGCAGGCAAAGGGCTTGAGGACAGCATAGACATGAGTGTGGCCTCACCCTGTGGCAGGCAGCAGGTTGGTATAAGGTTATGGTATTCTGGCTCCAGCACTTGAGTGTGGGGGGATTAGAGATTTGGCACACACATGCACTCTGGTTTCAGCCATTGACTATGCATGTGTGCCAAGGACCCTAACCCATCTTTCTCCTTGCAAGCCAGCTTGGGGCACCTGCTCCTAGGAATTGCCTGGTAACTGACGCCAGCCCTACCCTGGGGTTCCCACTTACTAACCCCATGACCATCTGACTAACACCCCCTGCCCTGCACCCCACATGGCTTGCTCTGGGCTTGTTCCTGTGGCTGCCCAGGAGGCTTAGATGGCATTGGCAGGGCCTCACTGCCCCTCCCCCACAG
Seq C2 exon
CTACCAAGGCATTCCAGGGCGTGCTGGAGCTTGAGGGGGTCGAGGGACAGGAACTGTTCTACACACCAGAGATGGCTGACCCCAAGTCAGAGTTGTTTGGGGAGACTGCAAGGAGCATTGAGAGCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041936-Agrn:NM_021604:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.559 A=NA C2=0.225
Domain overlap (PFAM):
C1:
PF0139015=SEA=PU(0.9=2.1)
A:
NA
C2:
PF0139015=SEA=FE(38.9=100)
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:
GACTTGAGCCCCCGGTGG
R:
CGTGCTCTCAATGCTCCTTGC
Band lengths:
266-678
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: