MmuINT0020601 @ mm10
Intron Retention
Gene
ENSMUSG00000021066 | Atl1
Description
atlastin GTPase 1 [Source:MGI Symbol;Acc:MGI:1921241]
Coordinates
chr12:69931538-69932321:+
Coord C1 exon
chr12:69931538-69931672
Coord A exon
chr12:69931673-69932216
Coord C2 exon
chr12:69932217-69932321
Length
544 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
TGCACTCTACTTTCCTGTAGGTT
3' ss Score
10.07
Exon sequences
Seq C1 exon
GAATCTGTTGATTGGGTTGGAGATTACAATGAACCATTGACTGGATTTTCATGGAGGGGTGGATCGGAACGAGAAACCACAGGAATCCAGATATGGAGTGAAGTTTTCCTCATCAATAAGCTTGATGGTAAAAAG
Seq A exon
GTATGACACTTTTTAAATAAAGTTATTTTTTTATTTTCAATGGTAACTTTGAAACCTTCTTTTAAAAATTGATTTGTCTATTTCACATAATGCTGCAAGGGTCAGAGTATTGTCCTATTGAATGATCCCTGTTTAACTCTTTAGTGATACCAGGAGTCAAAAATCATAATAAAGACAAAATAGCATATAACAAGCTGATATTTTTGGGGGGGGGAGGGCATGGGGGACTTTTGGTGTAGCATTGGAAATGTAATTGAGGAAAATACATAATAAAAAATATTAAAAATTAAAAAAACAAGCTGATATTTTTACATCGTCTCAATGCTAGGTTTTTATCTTAGATAATCAGAGAAAATTAAAAGTGACTGTACCCAGCTGCTAATTAATATCCTTTTATTTTTTTGTGGTATTCATGGCACATACAAGAAGTTACCTTTTAAGTATTCATTGATAATAGATGTTTTTAGTTCTTTTGTTGTTAATGGCATGGTAACCCTGGTACCTTGATTTTCTGTACAATGTAGTGCACTCTACTTTCCTGTAG
Seq C2 exon
GTTGCAGTGTTACTGATGGATACTCAGGGAACCTTTGACAGTCAGTCAACTTTGAGAGATTCGGCCACAGTATTTGCGCTTAGCACAATGATAAGCTCAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021066:ENSMUST00000021466:4
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:
PF0226314=GBP=FE(16.2=100)
A:
NA
C2:
PF0226314=GBP=FE(12.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATCTGTTGATTGGGTTGGAGA
R:
CTGTATTGAGCTTATCATTGTGCT
Band lengths:
240-784
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