MmuINT0104400 @ mm10
Intron Retention
Gene
ENSMUSG00000034593 | Myo5a
Description
myosin VA [Source:MGI Symbol;Acc:MGI:105976]
Coordinates
chr9:75167019-75169081:+
Coord C1 exon
chr9:75167019-75167230
Coord A exon
chr9:75167231-75168924
Coord C2 exon
chr9:75168925-75169081
Length
1694 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
CCCCTCTTGTCTTTGGGCAGCTA
3' ss Score
8.23
Exon sequences
Seq C1 exon
GACAAGGATAAATACCAGTTTGGTAAGACAAAGATCTTTTTCCGTGCTGGTCAAGTGGCCTATCTTGAAAAATTGAGGGCTGACAAACTTCGGGCTGCCTGCATCCGGATCCAGAAGACCATTCGTGGGTGGCTTCTAAGGAAGAGATACCTGTGTATGCAGAGGGCAGCCATCACAGTGCAGCGATACGTGCGGGGCTATCAGGCTCGATG
Seq A exon
GTAAGTCTCCTTATGGCCTCGTGAGTTCATGGTCCATTCTAGAACAGGTCTGAATGAGAAGATAGTGGCTCACTCATTATTAGTTTCAAAGCTTAGCAAATTAACTCAGAAGACAATTTAAAGGAATGAAATCTTACGTAGAGTTACAGTAATAAAGATCTGAATTGCTACCAACTTAGGTCCTTAGAATTTGTACATCTTTTGCTTTAACAGAGAACTTGAAAAAATTATATGTAAATTAAAATAACCACAGATATGAGACAGATAATCTTGACTCTACTGAGGAGCAATTAACTGAGAACATTTTAGCAGAGAATTACATTTTTTTAATTAGGTATTTTCCTCAATTACATTTCCAATGCTATCCCAAAAGTCCCCCATACCCATCCCCCCAATCCCCTACCCACCCACTCCCTCTTTTTGGCCCTGGCGTTCCCCTGTACTGGGGCATATAAAGTTTGCAAGTCCAAAGGGCCTCTCTTTCCAGTGATGGCTGACTAGGCCATCTTTTGATACATATGCAGCTAGAGACAGGAGCTCCGGGGTACTGGTTAGTTCATATTGTTGTTCCACATATAGGGTTGCAATTCCCTTTAGCTCCTTGGGTACTTTCTCTAGCTCCTCCATTGGGGCCCATGTGATCCATCCAATAGCTGACTGTGAGCATCCACTTCTGTGTTTGCTAGGTCCCGACATAGTCTCACAAGAGACAGCTATATCAGGGTCTTACAGCAAAATCTTGCTAGTGTATGCAATGGTGTCAGCGTTTGGAAGCTGATTATTGGATGGATCCCTGGATATGGCAATCACTAGATGGTCCATCCTTTCGTCACAGCTCCAAATTTTGTCTCTGTAACTCCTTCCATGGATGTTTTGTTCCCATTTCTAGGAAGGGGCAAAGTGTCCACACTTTGGTCTTCGTTCTTCTTGAGTTTCATGCGTTTAGCAAATTGTATCTTATATCTTGTGTATCCTAAGTTTCTGGGCTAATATCCACTTATCAGTGAGTACATATTGTGCGAGTTCCTTTGTGATTGGGTTACCTCACTCAGGATGATGCCCTCCAGGTCCATCCATTTGCCTAGGAATTTCATAAATTCATTCTTTTTAATAGCTGAGTAGTACTCCATTAGAATTACATTTTAATATGAAATACTGAAATATACCCCCTTTTCCAAGACTAAATACAGAATTAAATTAGAACAGTGGTGGAATGGTTTTAAAAAAGAGAGAGAGATACTGAAATATATAGACAGTTTTAATTTAGAGGTACAAGTAGAAGTGAATTAATGGTAAAGAACAGAACACCAAAACCAGCTCAGATTCAGGAAGTAATGTTTGAACAGTGATCTGAGATAACTCGTAAAGTGAGTTTGGAATTACAGTGTGCATCAGCTTGCTGTGTGGAGGGATCATAGCATGGAGCAGGGAGCCTGTCCTGGAAAGAGTAAAGCTTTATGAACTTCTTTTCCTTTTTGTAAAATGTGGCAATATGGGACATAGTGCTTTTCAAAATTAGGGAATCCCCAGTGAGAAAATACTTCAGAAGCTAGAGATTTCTGAACACATAAGTGAGTATAATGCTTATTTGTGGTGAATATAAGAATACAAACAGTGAGGTTCTGCTCAGGATACTGATAGTGATGGTTTGCAGTCTTGATGGCTGACAATGCACCCCTCTTGTCTTTGGGCAG
Seq C2 exon
CTATGCTAAGTTTCTGCGCAGAACCAAGGCAGCAACCACCATTCAAAAGTACTGGCGCATGTATGTGGTCCGCAGGAGGTACAAGATTAGACGAGCTGCCACGATTGTTATTCAGTCTTACTTGAGAGGCTACTTGACAAGAAATAGGTATCGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034593:ENSMUST00000123128:19
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:
PF0006316=Myosin_head=PD(2.1=19.7),PF0061222=IQ=WD(100=29.6),PF0061222=IQ=PU(81.0=23.9)
A:
NA
C2:
PF0061222=IQ=PD(14.3=5.7),PF0061222=IQ=WD(100=39.6),PF0061222=IQ=WD(100=39.6)
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:
ACAAAGATCTTTTTCCGTGCTGG
R:
CTTGCGATACCTATTTCTTGTCAAGT
Band lengths:
342-2036
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