MmuINT0168114 @ mm9
Intron Retention
Gene
ENSMUSG00000001525 | Tubb5
Description
tubulin, beta 5 class I [Source:MGI Symbol;Acc:MGI:107812]
Coordinates
chr17:35973573-35975246:-
Coord C1 exon
chr17:35974942-35975246
Coord A exon
chr17:35973682-35974941
Coord C2 exon
chr17:35973573-35973681
Length
1260 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CGTTGCTCTTCCCTGTGCAGTTC
3' ss Score
10.64
Exon sequences
Seq C1 exon
GCCCCCGGCCGCGCGAACGCGAGCCCCGCCCTGCGCGCCTTCCCTCCTGCGCTCGCCGGCCTCTTCTGCCTCTTAGAACCTTCCTGCGGTCGTGCTTGCATCTCGCTGCTGCAGCCTCCCGGGCTCCGGTCCATCCTTTCAGTCTGAGACCGGCCCAGAAGAAAAAAACCCCAAAAACCTTAATTTTCTTTCTTGTTCGGTACCTACATTGGAACCATCAAAAACAATTATTTCAGTAAACCGTAGCCATGAGGGAAATCGTGCACATCCAGGCCGGACAGTGTGGCAACCAGATCGGTGCTAAG
Seq A exon
GTAAGGACTTTAAAATTTTAGCTGAAATATGTAAAGATGAGAATTCTGTGTTAATTGTGAGCATTGTTCACGGAGTTCTTGCATTCTCCACCCGTCAGATTTGGCCCCTCAAAGTTTTTCACGTATAAATATAACCCATATTTGTAGCTAGCGTTCTGATATTGAAAAATGAGGAAATGTTTTTCTTGGCACATTTTCGGAAAGCTAATAAAAGAGCCTTTCGAGTTTAGGGAAAAGGAGAGGCTGAGGGACTGTGAAGAGCTGGTCTTAAAAGGGGTTTTCTAACGGTTCGAGGACTGGAGGGATGCGGAAACGATCCGAGACAAAGCCGAGGCGAGGTTTTCCCCTTGCGCCACCCCCACCCAGCCTGGAGGGCTCTACTGGAACAGAATGGAGGGGGGAAGGGGCGAGGTTTGGCGGGCAGCTGCAGAGGTGCCCGGTGCGCATTACCTCTCAACAAAGGCTTGGACACTCCATCGAACCCGCCATCCCAATGCTTTTTTTAGGTAATGACTCTGTATAGGGGCCTACTTTTACTTTTCATTGCCCTTTAGGGTGTGAGCGGTATGAAAGTGAGCTTTTCAAATATGTGAGACTGTCTGGGAGACTAAGGAGAGGGAAGGAAGGGAATAAAGATAGGCAATGGGGCTTTTTAAAGATTTTTCCCCCTTTTTTGCTAGCAATTAACAATGTAGCGGGGGAGGGGAGGGAGGAAGTGCGGCCGCTAAATTGTAGCCGAAGGGTGGGACCCTTTGGGGGCGGGGTTGGAGCCCCTGGCGCGCAGGGACAATGCGGCCCCTACCCGCGGGGGCGCACTGGCCCCGCCCCTCGAGCTAGGCCCCGCCCGCGCTGCTCCCGCCTTTGTGGTTTGCTGGAGGAGCGGCCCGCCACCGCAGTCACGTGGAGCACGTAAGGGGTGGGCGACTGCAGTGGCCGCACCTTTCTCCCCCAACTCTTTTGTGCTGGCCTGGAAGGGCGGTTCCTGGCTTCAGGAGCCAACCTGGGTGCAAAGCCAAATAGGTGGGCTCCAATCCGCCCACATAGAGGTTTATAGCGCCTGACCCACCCATCACCGGTCCTATGCCGAAAGGTTTTAGCCTTCCATCGCGTAGGTTCCTCCATGGGACTTCCGCAAGCAGATAACGGAATTGCAGTGTCTTCACCTCAGCCTCGTTTCAGCGTGTCTGGAATTGAAATGAGGGGCGGGAGGCATGCCTTAGGACTTGAGACATTGAGGCCTCGTTGCTCTTCCCTGTGCAG
Seq C2 exon
TTCTGGGAGGTGATAAGCGATGAACATGGCATCGACCCCACCGGTACCTACCACGGTGACAGCGACCTGCAGCTGGACCGAATCTCTGTGTACTATAATGAAGCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001525-Tubb5:NM_011655:1
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=0.135
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
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCTCTTCTGCCTCTTAGAAC
R:
AGTACACAGAGATTCGGTCCAG
Band lengths:
342-1602
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: