MmuINT0020618 @ mm10
Intron Retention
Gene
ENSMUSG00000059811 | Atl2
Description
atlastin GTPase 2 [Source:MGI Symbol;Acc:MGI:1929492]
Coordinates
chr17:79854554-79856263:-
Coord C1 exon
chr17:79856136-79856263
Coord A exon
chr17:79854611-79856135
Coord C2 exon
chr17:79854554-79854610
Length
1525 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TGAATCTTGTGTCTTTTTAGGCA
3' ss Score
10.38
Exon sequences
Seq C1 exon
ATATCGATGAAGACTTTAAACGGGAGCTTCGAAATCTGGTTCCATTGCTGCTTGCTCCTGAAAATCTTGTTGAGAAAGAGATAAGTGGATCGAAAGTCACTTGTAGAGATCTTGTAGAGTATTTTAAG
Seq A exon
GTAGGTGACCTCTAAGCTAAATGTCTGTCTCAAAAAGAAATGTAGTTTAACTTTTAACACACCTTTATGGATGAGAAATTTACTTTCTAGCAAAAAAACAATATACATTTTTCAACATTAAGGGTATGGAAGGGTCAGTTGCTAAAAGTACTTGGACAATCCTGAGGACCCAAGTTTCATCCTAGATAGCAAATAATAAGCTGGTATCTCACATAGTTGTGACTCCCTTGAGAGGGAGGAGACAGTTGGGGGTTGGATAGGTGGTTGCTTCCCAGCTCACTGAGAAAATAAGAGCCCCAAGTTTAGAGAAAGACAATGAATAAAAGGGATGTCAGAGCGTGAGAGAACACGTGTCTCCTAGTCTCTGCATGGTAGCTAGCGTAGGGTGGGCCCAGACTCGAGTGCATATAAACACAGATGGCTGTGCCTGCACGTGGGATGTACACACACACACACACACACACACACACACACACACGGAAACAGATAAATCTTTTTAAAAAGATGACAGCACATGGTGTCTTCTACTCAGTGACACTACTTGTTGTCAGAATCTCCTTCCTTTTCTGCATCTCTGTTGTGGAGAGAAGACCCATTCGCGACGTTGTAGCACGGCTCTGCCCTTGTGAGCAATGCCTGGAGTCGCTCTATAGCCCAGGCTCTCCCAGAGTCTTCCTGCAGAGTTCTCAGGACTAATAGGAGCTACAAGTGTCTGGGTTTTGAGTCTAGGTCAGTTACTTCTGGAGGTTTTCCTGCTCTGTTTTAGCATTTCTTGTTGGAACAAGTTGTTGATACAGAGTGAGTTGTACTAATAGCTAAGAGATAGGTGGGTGGAGAGCACAGCTGGGGACGCTAATGGGCTTTGCTCCCTGTTAGGTGCTCAGCACTTTCACGAGTCACTGTTTAATTATGAATTAAGTTTGAGTCCATAGAAAGTTGAGGTCAAAAACCTCGTGTTGGATGCTGTGCACTTGTCTTCCTCTTCCTCGTCCCTCCTTCCTCCTTTACTGTGTGTGGATTTCCTTTTTGTGTGGAGTGTGTGTGGATGAAACCCACACTCCCTGCCCCTCACCCCCACCCCAGCCCTCGCCATTTGTTCCTTGAAACTTGATGTATGTTTTAAAGACCCAGGCTCCTGCTCTGACTGCAAGTTAGGGTTTGAGTTCAAGTGTTTAAATGATGATTTAACATGCTCTCTCACATCTGTTTGAAGCATTGAAAGTGGAGAGAATGAAAGATTTCTTTTTATTTAATCGATGATACTTTACATATAAAACTTAAATGTGAAGTAAAATTTTAGATAAGTTGGAATTTAAAAAGTTTCTGAAGAGGATTTTATTTGGCAACATACCTATGTGTTAATATTCAGGATAGAATTGACTTTGTTGTACTTACAGTGTATGAGTTTTAAGGCCTAGAACTTCGTTTTTGTGGTGTGAACTATTATGTTTAATGATAATTCTTTGGGGGGACATTGTATCAAATTGTATTGTACACCAATACAGTGAATCTTGTGTCTTTTTAG
Seq C2 exon
GCATACATTAAAATATATCAAGGAGAGGAACTACCACACCCAAAGTCTATGCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000059811:ENSMUST00000068282:9
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=0.167
Domain overlap (PFAM):
C1:
PF0226314=GBP=PD(15.3=60.5),PF028419=GBP_C=PU(10.7=32.6)
A:
NA
C2:
PF028419=GBP_C=FE(13.7=100)
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:
TCGATGAAGACTTTAAACGGGAGC
R:
CTGAAGCATAGACTTTGGGTGTG
Band lengths:
182-1707
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