MmuINT1003997 @ mm10
Intron Retention
Gene
ENSMUSG00000041936 | Agrn
Description
agrin [Source:MGI Symbol;Acc:MGI:87961]
Coordinates
chr4:156185088-156185901:-
Coord C1 exon
chr4:156185551-156185901
Coord A exon
chr4:156185136-156185550
Coord C2 exon
chr4:156185088-156185135
Length
415 bp
Sequences
Splice sites
5' ss Seq
ACTGTACGT
5' ss Score
6.33
3' ss Seq
ACCTAACTTTTCCCCCCTAGACA
3' ss Score
9.61
Exon sequences
Seq C1 exon
GAATTCTTCTTATCTCCTGCCATGAGCCTGGAGGGCTGGGGAGAGGGCCCGGTGCTCCCCTAGCCACAACTGGCTAAACTTTGCTATCACAGCTGCCATCTGCTGCTCCAGAGCACCCAGCATGGGGGGAGTAGCTCCGAAGAGGCCTAAAGGCCCTCCATAAGAACGCCCCACACCCCCAGGGACTGGGCTAGAGCCGTATCATGCCTCCTCTGCCACTGGAACACAGACCCAGGCAGCAGCCTGGTGCCTCCGTGCTGGTTCGGTACTTCATGATCCCCTGCAACATCTGCTTGATCCTCTTGGCTACTTCTACGTTGGGCTTTGCGGTGCTGCTTTTCCTCAGCAACT
Seq A exon
GTACGTGGCTGCTGGTGTACCTCACTGAGCCCCTCATCTCAGTTACCAAGGGTTTCGGGAAGGCGGCGTCAAATCAAAGCCTGGGGTTGCTGCGGAAGGGCGGCTTTTGCTTGTGGGTATTGAATAGGTCATACCAGATCCCTGGCCTGTGACAACCTATTCCTAGCTTCCTAACGGTATAGAGCTTCATCCCGAGCTGCAGGGATGAGATCTGGCAAGGATGCATCAGTGCTGGGATTAGAAGCAGGCCAAGATCTTGACTTACCCAGAGGAAGGTTGCTGTGCCGTTGGCAGAGTCTGCCCTGCCTTGCTCAGTGACTTTCCAGCCTTACTGATTTTAACTGCAATCTTGAGAAATGGGTATGAATGGGCAAAGTACCTTCCTTCTCAAAGGAACCTAACTTTTCCCCCCTAG
Seq C2 exon
ACAAACCTGGGATCCACTTCACAGCAGCGCCTTCTATGCCTCCTGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041936:ENSMUST00000105574:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.160 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0314610=NtA=PD(1.6=11.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCCCCTAGCCACAACTGG
R:
CATCAGGAGGCATAGAAGGCG
Band lengths:
346-761
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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