MmuINT0166393 @ mm10
Intron Retention
Gene
ENSMUSG00000039826 | Trub2
Description
TruB pseudouridine (psi) synthase family member 2 [Source:MGI Symbol;Acc:MGI:2442186]
Coordinates
chr2:29786476-29788502:-
Coord C1 exon
chr2:29787503-29788502
Coord A exon
chr2:29786608-29787502
Coord C2 exon
chr2:29786476-29786607
Length
895 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CTGTGTTCTTTTGTGCTTAGGTC
3' ss Score
10.88
Exon sequences
Seq C1 exon
GGGTGGTTGGGATGTGGTCCGGGTACAGCAGGCGGGCGCCATGGCTCCCGGCCCTGAGGGGTACATCTGCGAGCAGAAAAGAGGTAAAGGTGAGAGGAGTCCGGTCCCTCTGGTCGCCGCGGACACTGGAATCAGAGCTGCTCACCTACAGCTGGCCGCGTACGGGGCCGAAGACTGCGGTGGAGGCGCAGGGAGCGAAGCAGCAGCAGGGTCGCCATGGCAGCGGACGTCCGCGTGGTTAGGCGGGGCTCCGCAGGTACTACGGAGGCCCGAGAAGTCAAAAGACTCCTGGGACACTGCACTCACTGTGGCTTTTTGATCGGAGATGTTGTAATATGGACAGGAGCATGAGAAGGAAAGCCACAAGATCTGTTTGCCACTGAAGTAAAACAACTGCTGTGAGCCAGGCGTTATTTATAACGTAGGCCTGTCAACCCAGCATTTGAAACCTGGAGGCCGTAGGATCAGTTCGAGATCCTTCTTGGCTATTTCTTAAGTACGAAGGCAGTACTAGAGACCTTGTCTCAAAAACCAAGCCTGATGTGAATTACTCGTCACTCCAGATCTTGGAAAAGTGGAGACAGAAAAGTAATGAATTCTCGGCAACTTAGCAAGTTTGAGGGCAGCCTGGGATATATGAGAAACAAACAAACAAAAAACTCCTGAAAAGAATTCAAAAATAACATAACCGAGAATTCGGTTGCTCGATATCCGGCCCTATTTTCTTCTCCATCTCTTATTTCCCCCCCGGAGGGCAATAAGAAAAGAACCTCTTCCTGCCAAGGAAACAAGGCGGCTACCTACAGTAGGGACCACATTTGGGAAAGGACCACGCAGCACTTCCGCCCGCATCCCCGCTTCTGGATGATGTTGAACCGCTGAGTTCCAGCCATGGGTTCTTCTGGCCTAGCTCGGCTGCAGGGGCTCTTCGCTGTCTATAAACCTCCGGGGCTGAAGTGGCTGCACTTGCGTGAGACCGTGGAGTTGCAACTGCTTAAAG
Seq A exon
GTGAGAACTCCGACGCGGACCCACGGTTTTGCTTTAGTTCTTTCTGATGTGGAGTGAGGTCACGTGGTTCGTTTGCCGGGTTGTAGCTGTTTCTTGTTTGTTTGTTTTTTTTCTCTTGTACACATTTCGTTACTACCCACTCTCCGCTATTTTCCTTTAGAGAAATTCATTCTATAGTGTTGGGTTTTTTTTCGCGGTTTCTGTTACAGAGTTAGAATTTGAACTTTTTTTTTTTTTTTTTTTTTTTTTGCCTTTTGAGACAGGGTCTTTTCTAATTAATCCGACCTTGAAATCAGTGAGGCACTGAGAATTCTGACTCTCCTGACTCCACCTGCCAGATGCTGGGATCACAAGCGTGACCACCACCCCGACCCTCAAACACCAATTTTTTTCTTTGCCTTTTTTTCCTTTCTTTTATTTTCTTAAAAACTGTCATGTAGCCTCAAATTTGCTATGTAAGATGAAGATAACCTTGAACTTTTGACTGTCCTGCCTTCACTACCCAAGGTCTTAGACTACATCTGTGTAGTACCACCTCCCATTAGGGTGCTGGGGATGGAACCCGGGGCGTCTTGCGTATTGTGCAAACACTCCATGAATTGAGCTACACTTCCAACCTAGGATTTTTGTTTTGTTTGTTTGTTCTTCACTTTTTAGAGAATGGTTTCTCTGTATACCCCTGGCTGCCCTGGAAATAACTCTGTAGATCAGTCAGGCCTTGAATTCAGAGATAGGCCCGCCTCTTGCCTCCCCAGTGCTGGAATTAATGATACCTGGCTTCTGAAGGAGTCATAGTACGTTTTCTACGATACACAAATCCATCTTCTATGCTACCATCTCTCTACCCCTTCTCTTGCGGGTTGGAAAAGTACTGACTGTGTTCTTTTGTGCTTAG
Seq C2 exon
GTCTCAATGCCCAGCAGCCTCCTGCTCCTGATCAGCGTGTTCGCTTCTTGCTAGGCCCTGTGGAAGGCAGTGAAGAGAAGAAGTTGACTCTCAGAGCCACCAATGTACCCTCCCTCACCACCCACAGACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039826:ENSMUST00000048044:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.024 A=NA C2=0.365
Domain overlap (PFAM):
C1:
PF0084917=PseudoU_synth_2=PU(17.1=70.3)
A:
NA
C2:
PF0084917=PseudoU_synth_2=FE(28.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGCTCGATATCCGGCCCTAT
R:
GAACACGCTGATCAGGAGCAG
Band lengths:
342-1237
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