MmuINT0168101 @ mm10
Intron Retention
Gene
ENSMUSG00000058672 | Tubb2a
Description
tubulin, beta 2A class IIA [Source:MGI Symbol;Acc:MGI:107861]
Coordinates
chr13:34074301-34076288:-
Coord C1 exon
chr13:34076178-34076288
Coord A exon
chr13:34075529-34076177
Coord C2 exon
chr13:34074301-34075528
Length
649 bp
Sequences
Splice sites
5' ss Seq
TCGGTATGT
5' ss Score
9.22
3' ss Seq
ATTCTCTTTTTCTCTTTCAGGCC
3' ss Score
13.15
Exon sequences
Seq C1 exon
GCAACAAATATGTACCTCGGGCCATCCTAGTGGACCTGGAGCCGGGCACCATGGACTCAGTGAGGTCGGGACCATTCGGCCAGATCTTCAGGCCAGACAACTTTGTGTTCG
Seq A exon
GTATGTTGTGATGCTCCATGAGAGCTGGCCAGATGACTCACTCCCTTCCTAGCAGCCGTGGGCTTTACAGTTCTGTGTGCAGCATCCAGCTGAGCCTGTGTCCCACAGACCACAAGTCCTGGCCTAACCTAGGCAGCTGACAAGATCATGTCTGTGGTCACTCTTGACAGCTCAGAGGAGAGTGTGGGCCTGGTAGAGGCTGTGCAAGGCCTCTGTGAGGAACAGTGTCTGGGGGCAGGGGAGGAGGGGATGAAAGCCTTCAAAGAGGGCATTACAGGCTGCAGGGGATTTCAAAGGGCTTCTGATGCCAGGCAACCACTTCAGTGACCAAGGTGAAGCCCAAATGCTTACAGCTGCCTTCCCTGCCTCTTTAATTATACCTAATTAAGGGTATTTACAGAATGCTCTCTGTGCTTAAGTTTAGAAGCTACTGAGTATTGTTAAAATGTGTCCTCTTCCTTGATTCTTTCTTTATTATGATCCTCAAGGTTTTTGAGGTCCCTGGATACACTGACAATATTTCTTTCTCATAAAAGTATATCTAAAAGACTACTGAATGTTCTCTAAGGCCACTTCTACCATTTCCTCTACAGTCCAAGGACACCTCCCTGGATTCCTAACTGTCTAATATTCTCTTTTTCTCTTTCAG
Seq C2 exon
GCCAGAGTGGTGCAGGAAATAACTGGGCAAAAGGCCACTACACAGAGGGGGCCGAGCTGGTGGACTCTGTCCTAGATGTGGTGAGGAAGGAGTCTGAAAGCTGTGACTGTCTCCAGGGTTTCCAGCTGACCCACTCACTGGGGGGAGGCACTGGCTCAGGCATGGGGACCCTGCTCATCAGCAAGATCAGAGAGGAGTACCCAGACCGCATCATGAACACCTTCAGCGTCATGCCCTCACCCAAGGTCTCTGATACTGTGGTGGAGCCCTATAATGCCACCCTCTCAGTGCACCAGCTGGTAGAGAACACAGATGAAACCTATTCCATTGACAATGAGGCTCTGTATGACATCTGTTTCCGCACCCTGAAGCTGACCACACCCACCTATGGCGATCTCAACCACCTGGTGTCAGCCACCATGAGTGGAGTGACCACCTGCCTGCGCTTCCCAGGCCAGCTGAACGCAGACCTGCGCAAGCTGGCCGTGAACATGGTGCCATTCCCACGCCTGCACTTCTTCATGCCAGGCTTTGCACCTCTGACCAGCCGGGGCAGCCAGCAGTACCGAGCCCTGACGGTGCCCGAGCTGACCCAGCAGATGTTCGACTCCAAGAACATGATGGCTGCCTGCGACCCTCGCCATGGCCGCTACCTGACCGTGGCCGCCATTTTCCGTGGCCGCATGTCCATGAAGGAGGTGGATGAGCAGATGCTCAACGTGCAGAACAAGAACAGCAGCTACTTCGTGGAGTGGATCCCCAACAACGTCAAGACGGCCGTGTGTGACATCCCTCCTCGTGGCCTCAAGATGTCAGCCACCTTCATTGGCAACAGCACTGCCATCCAGGAGCTGTTCAAGCGCATCTCGGAGCAGTTCACTGCCATGTTCCGGCGCAAGGCTTTCCTGCACTGGTACACGGGTGAGGGCATGGACGAGATGGAGTTCACCGAGGCGGAGAGCAACATGAATGACCTGGTGTCTGAGTACCAGCAGTACCAGGATGCCACGGCTGATGAGCAGGGCGAGTTCGAGGAGGAGGAGGGTGAAGATGAGGCTTGAGAACTTCTCAGATACAGTGTGCACCCTTAGTGAACTTCTGTTGTCCTCCAGCATGGTCTTTCTATTTGTAAATTATGGTGCTCAGTTTGCCTCTGTCAGAAATTCACTGTTGATGTAATAGTGTGAACCTCTTTCAAGATCACAGTATTGTCTCAGAAATCTATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058672:ENSMUST00000056427:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.026 A=NA C2=0.102
Domain overlap (PFAM):
C1:
PF0009120=Tubulin=FE(16.7=100)
A:
NA
C2:
PF0009120=Tubulin=PD(59.0=37.0),PF0395312=Tubulin_C=WD(100=34.7)
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:
ATGTACCTCGGGCCATCCTAG
R:
ATCAGAGACCTTGGGTGAGGG
Band lengths:
356-1005
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