MmuINT0020612 @ mm10
Intron Retention
Gene
ENSMUSG00000059811 | Atl2
Description
atlastin GTPase 2 [Source:MGI Symbol;Acc:MGI:1929492]
Coordinates
chr17:79864703-79865176:-
Coord C1 exon
chr17:79865042-79865176
Coord A exon
chr17:79864808-79865041
Coord C2 exon
chr17:79864703-79864807
Length
234 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAAA
5' ss Score
1.18
3' ss Seq
TAAATTTAACGAATTCCTAGGTG
3' ss Score
4.41
Exon sequences
Seq C1 exon
GATTCTCAAAGCTGGATTGGTGGAAACAATGAACCCTTGACTGGCTTTACGTGGCGAGGTGGTTGCGAAAGAGAAACAACAGGCATACAAGTTTGGAATGAAGTGTTTGTGATTGACAGACCTAATGGAACAAAA
Seq A exon
GTAAAATTCTACTTATACTTTGCTATTTTCTCCTGTATTCTTTTCTTGAGCAATTTTCTGGTATTAAAATTTAAAAGAACACAAAACTATTAATGATTAATATGTTAAAATGTACAATGGTATGTAAATACTTTTCTTGACTTAATTACTGCTTTGAACTTTATTAATGTATGATTTTTGTAGGCATTTTTGGTGATTCTTTTACTAAGTATTTTAAATTTAACGAATTCCTAG
Seq C2 exon
GTGGCTGTGCTGCTAATGGATACCCAGGGTGCCTTTGATAGCCAGTCAACCATTAAAGACTGTGCGACAGTGTTTGCTCTGAGCACTATGACCAGCTCTGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059811:ENSMUST00000068282:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.044 A=NA C2=0.004
Domain overlap (PFAM):
C1:
PF0226314=GBP=FE(16.2=100)
A:
NA
C2:
PF0226314=GBP=PU(17.1=96.7)
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:
TTCTCAAAGCTGGATTGGTGGA
R:
GCACAGAGCTGGTCATAGTGC
Band lengths:
236-470
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