MmuINT0020622 @ mm10
Intron Retention
Gene
ENSMUSG00000024759 | Atl3
Description
atlastin GTPase 3 [Source:MGI Symbol;Acc:MGI:1924270]
Coordinates
chr19:7530520-7532447:+
Coord C1 exon
chr19:7530520-7530591
Coord A exon
chr19:7530592-7532015
Coord C2 exon
chr19:7532016-7532447
Length
1424 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
TGTGTTTTTGTTATTTTTAGATT
3' ss Score
11.03
Exon sequences
Seq C1 exon
GCCACTGCTGAAGCCAATAATTTGGCAGCTGCAGCCTCTGCCAAAGATATTTATTACAACAACATGGAAGAG
Seq A exon
GTATGTGGGTAACACCGTGTTCTGAAGTGTCATTTTCCCAGCATGGCTGCTGACTTCAAAGGCCCAAATTTGATCCTCCTCAATGTATCCTTTTTGTTTGTTTGTTTGACACAGGGTCTTATGTAATAGGCTGGCCTGAGAATCACTGTGTTAGTGGAAGGTGTCTGATTGTACTGCCTAGACCTCACTAATGCTGTGGGCACAGGAATGTGCTTTAAAAGTCTGTTTTCACTTATTAATCCTTGTGTATGTATGCCATAGACATGGGTGCTCTTGGGCCAGAAGAGGGCATGGGATCCTCTGAAGCTGAAGTTCCAGGTGGTTGTGAATGGCCTAATGTGTGTGTTAGAAATGCAACCTGCTTGTCTAGAAAAGCTGGAAGCCCTCCTTTAATTCATGAGCTGTCGCATCTTAAGATGATGAGTTAGAAAGCTGTCTTTCAGGTCACCCTAGTAATTGGGATGCTCCTAATTATTACTTTTTAAGTTTAATCTTTCTTTTCTTTTGAAACAGAGTCTTTCTATGTAATTTGGATCTTCTAGTTATTTTTATTTTTGTCAGGCAGAGTTGTGATATGTAGTCCAAGTTGGCCTCAGATTCATAGCAATTCTTTTGCCTCAGTCTCTTAAGTCCTAGACAAATGTGTGCTGCCATATCTCTTCTGTTAAGATTTATTATTTATTTATGTGTATATCTCTGGAGTGGGTACCTGAATACACAGTCAGACATTAGATCTTCTGGAGCCCTAGTCACAGGAGGTTTTGAGCTTTATGATGTGGGTGCTGGGAACTGAACTCTGGTCCTGCAAGAGCAGCAAGTGTTCTTAACTACTAAGCCATCTCTCCAGCCTCCTAGTGTCTGGTTCTTAACCATTTCTAACCAAGCTTTTAATTAATCTTTATATTTTTATACAAAGACTTGCTTTGTGGCTGTGGTTGGCCTGAAATATGTTATGTTGACCAATTTCACATTAAGCTTGTATGGATCTCTTGCCTCTGCTTTCTAAGGGCTGGGATTATAGGCATATACTAATATGTCTGGCTTTGGTCTGGGATATTTGTCTTTTCTGACTTCCCGTTTAAGCAGAATCTCACGTAGCTTAGGTGGGCCTCAAACATTTCATGTAGCTGAGGATGACTTTGAATTTTCTGATCCTTCTGTAACTACTTGTGGAAGGTTGGGATTACAGATATGTACCACCATACTGATTTGTATGATATTGGGATTAAACCAAGGGCTCTGTGCATACTAGGCAAGTACTCTAACATATAGGTTATATCTTAGTCTCTCTTGAATATTTTCTGAAGTTAATTTCTAAGCTTTTTTTCTAAACTCTTAAGAGCATTCAAATCTTTACTGTGACTTTTTACTTACTTTATTTGGCATGTACAAGAATATTCAGCATGTGTTTTTGTTATTTTTAG
Seq C2 exon
ATTTGTGGGGGAGAGAAACCTTATTTGTCTCCAGATATTTTAGAAGAGAAGCACCTAGAATTCAAACAACTTGCTCTGGACCACTTTAAGAAGATCAAAAAGATGGGTGGGAAGGATTTCAGCTTCCGTTACCAGCAGGAACTGGAGGAGGAAATCAAAGAACTGTATGAGAACTTCTGCAAGCACAACGGCAGCAAGAATGTCTTCAGCACCTTCCGAACCCCTGCAGTTCTGTTCACAGGCATAGCAGCATTGTACATAGCCTCGGGCTTCACGGGCTTCATTGGGCTTGAGGTTGTGGCCCAGCTGTTCAACTGTATGGTTGGACTGCTCTTAATAGCACTCCTTACCTGGGGGTACATCAGATATTCCGGGCAGTATCGTGAGCTGGGTGGAGCCATTGACTCCGGTGCAGCATATGTGTTAGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024759:ENSMUST00000025668:11
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:
PF028419=GBP_C=FE(18.1=100)
A:
NA
C2:
PF028419=GBP_C=PD(53.5=47.2)
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:
CCAATAATTTGGCAGCTGCAGC
R:
AACCTCAAGCCCAATGAAGCC
Band lengths:
356-1780
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