MmuINT0013100 @ mm10
Intron Retention
Gene
ENSMUSG00000024397 | Aif1
Description
allograft inflammatory factor 1 [Source:MGI Symbol;Acc:MGI:1343098]
Coordinates
chr17:35172285-35172689:-
Coord C1 exon
chr17:35172515-35172689
Coord A exon
chr17:35172347-35172514
Coord C2 exon
chr17:35172285-35172346
Length
168 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGGG
5' ss Score
5.76
3' ss Seq
TTAACCTCTGTACCCCTCAGGAG
3' ss Score
8.03
Exon sequences
Seq C1 exon
AAGCTGATGTGGAAGTGATGCCTGGGAGTTAGCAAGGGAATGAGTGGAAAGGGGAAGTGTGAGAACGGTCCCAGAAGAGACTGGGGAGCTGGTGGAGAGAGGACCCAGCGGACAGACTGCCAGCCTAAGACAACCAGCGTCTGAGGAGCCATGAGCCAAAGCAGGGATTTGCAGG
Seq A exon
GTAGGGAAGGTGGACCCCATAGTGTCATGAGCCAGCGTGAGTCAGGCCTGGCTTGGGGAGCCAGGGGGGCAGCTGGAGGATCTCAGAGGGCAGCACTTGGGTAACACCTGGGCTGGGCACGGGGAAGAGGAGAGGAAAGGAGGGGTGGTTAACCTCTGTACCCCTCAG
Seq C2 exon
GAGGAAAAGCTTTTGGACTGCTGAAGGCCCAGCAGGAAGAGAGGCTGGAGGGGATCAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024397:ENSMUST00000173324:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.236 A=NA C2=0.071
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF134991=EF-hand_7=PU(8.9=38.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGATGTGGAAGTGATGCCT
R:
TTGTTGATCCCCTCCAGCCTC
Band lengths:
234-402
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