MmuINT0168099 @ mm9
Intron Retention
Gene
ENSMUSG00000058672 | Tubb2a
Description
tubulin, beta 2A class IIA [Source:MGI Symbol;Acc:MGI:107861]
Coordinates
chr13:34168418-34169877:-
Coord C1 exon
chr13:34169742-34169877
Coord A exon
chr13:34168527-34169741
Coord C2 exon
chr13:34168418-34168526
Length
1215 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGC
5' ss Score
7.93
3' ss Seq
TGGGATTGTCTTCATTTCAGTTT
3' ss Score
6.87
Exon sequences
Seq C1 exon
TGGTCTTTTGCGCTCCTTAGCCCTCTGTCCACGCACTGCTCCGAGGGCAAGAGCCTCCACCCCTTCTACAACCAGCACCATGCGCGAGATCGTGCACATCCAGGCGGGCCAGTGTGGCAACCAGATCGGCGCTAAG
Seq A exon
GTGGGCTCACCCCTAGGGAAGAAATGGATGAGGTAGTCCCATCCGGTCAGGGTCCCAAGGTTGCGTGGGGAGAGGGGTAGGGGGGGGTGTCGCGGAAGCAGGCCGAGCCTAGGGGATCCAGAAGAGCCCCGGCTGGTGTCGCATTCCACCGCTGGCTACTGGGCGGGCCGGGTCCTGAAAGCCGACCAACTTGCCAGGATTGGTGCGACAAGGGTGTCTTAAATTAAGGTCCATTACATTGCTTTGGGACACAGCCCTTCTGCGGGGTGCAGCTGACATTAGTCTGGGTTTTTTTCGTGTCTGAAATTTGGGTTGGGGGGGTCACTACATGTATTGAAAAAAATCTCATGTCAAATGTAATTCATATATATATATATATTTCTGTCATTTGAATGAAAAAAATGCAGTGTCATTGGGTTGACAGATGTTACAGAGGCGTGTCTTTGGGCCAACAGACGAGGGTGTTAGACAAATTCTCTTACAAGGGCTCGTTTAGATGTGACATAAAACATTATGGTCCTCTTTTTTCTCTGCAAGACTGCTTGGAATGGGGGCTGTGAGACCCGACGGCAGTGGGGAGACAGCAATGGGTATTTAACATGGGTGTGGGCGGGTGCCTGCACAAGGACATGGTCTCTTTCAACACCGCCATATTGCCCACCCAACCTCCCCACTCCCTTTCCTGCTGCCAAGTCACAATGGAGGTTACATCCTGAGGATGGCCAGCTTTTTCCCGGGGCTGCCAGACGCCCTCTCAGGATTGTACTGCCCATCCCCGAACATTCCTAGCCAGGGTCAATACCCGAAGCCAATATGTAGGTCAGTGGTATAAAACTGGGCTGTTGAAAGCTGTCATGGAGTCTGTGCCAGCAGCCATTGATCCCTGGAGGCACAGGGGGCGGGGCACCTGATTTTCCCTTCTGCCTTTCCCATCCATCAGCCTGTATGTGTAACATTCAGCCTTGCCTGGAGTGATAGAAAGCAGCTGCCTCTGCAGTTCTGCGAGATCCGCTGTGCCCACTTCCTTCTCCAGGCTCCTCCCAGCCCTGCATCTGTGGTCATAATATGGCCGATGCACTGCGCATTCCCAAGACCCTCTGCAGCAGCAGCTGCTGCCCAAATACATGGAGGCCCGCAGCCCACTAGGCTCTTGCCCTGCTGTCTTTCTGGTGACAGAGAGATTCTAAGCATGATGTGGGATTGTCTTCATTTCAG
Seq C2 exon
TTTTGGGAGGTGATAAGCGATGAGCATGGCATCGACCCCACTGGCAGTTACCATGGCGACAGTGACTTGCAGCTGGAGAGGATCAATGTGTACTACAATGAAGCTGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058672-Tubb2a:NM_009450:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.108
Domain overlap (PFAM):
C1:
PF0009120=Tubulin=PU(7.2=84.2)
A:
NA
C2:
PF0009120=Tubulin=FE(16.2=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:
TGGTCTTTTGCGCTCCTTAGC
R:
CAGCAGCTTCATTGTAGTACACA
Band lengths:
245-1460
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: