MmuINT0137261 @ mm9
Intron Retention
Gene
ENSMUSG00000041199 | Rpusd1
Description
RNA pseudouridylate synthase domain containing 1 [Source:MGI Symbol;Acc:MGI:1919186]
Coordinates
chr17:25866013-25868401:+
Coord C1 exon
chr17:25866013-25866114
Coord A exon
chr17:25866115-25867313
Coord C2 exon
chr17:25867314-25868401
Length
1199 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TCCCGTCCCTGATCCCATAGGCC
3' ss Score
10.87
Exon sequences
Seq C1 exon
GTTGTGAGAACCCAAAGCCAAGCCTCACAGAGCTGCTGGTCCTGGAACACGGCCTATATGCTGGTGACCCTGTGTCCAAAGTGCTGCTAAAGCCACTTACAG
Seq A exon
GTATGTCCAGGGCAGGAGTTCATCATATAAGAAAGGACCCCGAGGTATAGGCATTGTGGCCTGCCTGGGTCTATACTAGGTGTGCGGGCAGAGCCGATAGCAAGATCTTTGCTGGTGTTTGCATGTACCCTGGCTGTCAAGCTGATCTCTCTGGCTAGATCAAGGGTCTCCCTGACTGTGCCCTCACGGCCCACCCCGACCAATCTCTTGACCTGAGTCCCAATGTCTGATTTGTAGCAAGAAATATAATGAATCCCATACCAAGGGCCTGCCCCACCCTGCCCTGCCCTTCCTTCGCAGTAGCACAGATCTGCAAAGCAGCTAATCAGAAGAGAACCGTACTTTTCTTTCTTTCTTTTTTTCTTTCTTTCTTTTCTCTCTGTGAAGCTTTGACTGCCTTGGAACTCACTCTATAGACCAGGCTGGCCTCGAACTCTGCCTGCCTCTGCCTCTGTCTCTCCAGAGGGACTAAAGGCAGGCGTGTGCCATGACCGACTAGCAAGGGATCCATCCTTTAAAAAAGAAGACTGGGTAAGCAGGTGTGGTAGCATTTGTAGCACCCTAGAGATAGAGGCAGGAAGATCAGAAGTTCATACCTATCTTTTAACTACGAAGGCGCTCTCTGCCAAGCCTGACAGCCTGAGTTGGAGTCCCAGACAAACATGGTGGAAGGAGAGAGGAGAATCTTAGAAGGTGTCTTCTGAGCATTGTGAAATGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAAACAGGCAGATCTCTGTGAGTTTGAGGCCCATCTGGTCCAAGACAGCCAGGGCTAGTTTGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAAGGCTGCACAGAAAAGAAAAGAAAAAAAAAAAATATGTATATATATATATATATACCCTGTCTCAAAAAAAAAGTTGTCTTCTGATTTACTTCAACAGTGTAGCATCAAGCAGGCACATGTAGGAACACAACACACACACTCAAAATTAAAATATACTTTAAAAAAACTTTAAAAGGAGAAAGAAGAGAGTTTATTCCTCAACACTGTAACACACAGCAGCAAGCCGGGGGGCTGCCCGGAGACTCCGCAGCCAACCCAGAGAACTTGTTGGATACTGTAAGAGCAAGGGATGTGACAAAGAATGGTTTTCCTCCCAGCCTGACCTCCCGTCCCTGATCCCATAG
Seq C2 exon
GCCGGACACACCAGCTTCGTGTGCACTGCAGTGCCCTTGGCCACCCTATCGTGGGTGACCTGACTTATGGCCAGGCTGAGGACCAGGAGGACCAACCTTTCCGCATGATGCTGCACGCCTTCTACCTACGCATCCCCACACAGGCAGAGCGCGTGGAGGCCTGTACGCCTGACCCCTTCCTGCCTGCCCTCGATGCCTGCTGGAGTCCCAGTACCTGTGTTCAACCCCTTGAACAGCTCATCCAGGCCCTGAGGACTGACCCTGACCCAGACCCTATGAGTGGAGGGCCAAGGCCCTGCAGCCCCTCCACCCCACAGCCCAGGCCAGGTCGGCCCCCTCCTGAGACTGAGGCACAGAGAGCATCGTGCCTGCAGTGGCTATCAGAGTGGACACTAGAGCCGGACAACTAAGGGCCTCTGGGCTTTGGGGGTTGAGAACCACACCATCCAGCAGCTAGGCAGCCATGATTGCTGAGGACAGGGTTTTCGGGCAGTGGGAGAGATGCCCAGTAGGTAAGTCTTCTCTCGCTCGGCATTTCTCCAGAGGAAGCTCAGGTTTTCCTTCTGGTACAGCATTCTGCCTCTTTAGCCCCAGGCTTGCCCAAACCCCTAGCCAGGAAGGGCAAGGCCAGGAACGAGGATCCCCCAGGGCCCCACAGTGCCTGAGAAGGACCATCCTGGCATTAGCCTACCTGGACTTGGGTCACCTGCAGCCCCCAACCTGTCTCTTGCTGCCCGCCACTGTCATGTGCCTTTGCCTTTCCTGAACTCTGCCAGGGCCTCACCTCCTCTGCCTGCATCTAGCGCTTGGCCCCAATGCATGGGAGTGTGTTGGGGCATCTACAGAGGCATCCTCCATGCATGCCCAGTCCTCTAAGCCTGCCATGGATGCCGCTTCTGTTCTATGGGCTCCTAGCTGGAGCGTTGACATGTCACCACCTGCCTGGCTTCCACATAGCCATAGATTATCAGCGCCAGCCTTCGGGTCCTCTCCTGGGAGCCTTCTGGGCCTCACATGTCTGCCACAACACAGCCACAGCACCCTGGCTGTAGCTAGGGTCTAGGATTAAGAATAAATGTTCAGTGATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041199-Rpusd1:NM_028009:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.419
Domain overlap (PFAM):
C1:
PF0084917=PseudoU_synth_2=FE(20.5=100)
A:
NA
C2:
PF0084917=PseudoU_synth_2=PD(6.6=8.0)
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:
GGAACACGGCCTATATGCTGG
R:
CCTCCACTCATAGGGTCTGGG
Band lengths:
345-1544
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: