MmuINT0115667 @ mm10
Intron Retention
Gene
ENSMUSG00000004872 | Pax3
Description
paired box 3 [Source:MGI Symbol;Acc:MGI:97487]
Coordinates
chr1:78195251-78197134:-
Coord C1 exon
chr1:78196665-78197134
Coord A exon
chr1:78195487-78196664
Coord C2 exon
chr1:78195251-78195486
Length
1178 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
CTTTCGCCATCTCTTCCCAGTGT
3' ss Score
8.04
Exon sequences
Seq C1 exon
TCCCTAGTCCGGATCCCTGCACTCGGTGTCACGACGGGAGGAGACTTGGGACGTGTTCCTGCCTCGTCACCACCCTCCCTCACCCGATCTTCGCGGTGCAGTGAGCACCTTTGCCAGTAGCCCCAGCTGAGGGGCCGATCTGCTAGACTCGCACCAAACTCGTCCGCCCTGGGCTTGGGATCCTGCACTCAAGGGACTCCTCTGGAGCCTGTGGACTTGGATCTATTAGCGCCCCCCTCCCCGCGCCCCGCCTCCCTCTCTGGCCTTTTTTGGGGGAGGAGCTCTCCGAGATCCGGAGAGTTCCCGAGGGTCACCCGCCGCACTGTGCTCGCTTTTTCGTCTCGCCTTCACCTGGATATAATTTGCGAGCGAAGCTGCCCCCAGGATGACCACGCTGGCCGGCGCTGTGCCCAGGATGATGCGGCCCGGCCCGGGGCAGAATTACCCACGCAGCGGCTTCCCGCTGGAAG
Seq A exon
GTATGTTAGGGCCTCAGCTCGTCCGGATCCCCGGGCCTGGGATTGGCTGCCGCACCCCAATCCTGGTCTCCAGGGCCTCCACTCGTGCCTTACCGGGAGCCTCTTCCCGTGGTACTTCTCAACCCAAGAAGCAAAAGTGGGGAGGGGGTTCTCGTGGAGAGCGGGAGAAGCCCCATTTCACGTTCTGGCTGCAAACGGAGTGCTAAGCTCACTACAAGCTCTCGGAGCTTGCCTGGCCTGCTCCTGCCGGCTCCACTTTGCCCTGTTGTTTCGGAATTGCTGCCGTGAGAAAGGTGAACAAGCTTCGCAGCGCCGGAAGCAAGTTCTCTTTCTGTTCACCTAAAGTTGCTACGAAATTGTGCGGGCTGCGTTCACTTTTGAATAACTACTATTAGTTCGGCAAGAATTTTCCTGCTGTGAAAAATTCTGGTGGCCCTTCCTAGTTGAAAAGTTTTAGCATTGATTAGCAAATTCCACTCAACTCAAGTGGCATCTCGAAGTTTCTAAAATGGTTGGCAATGCCTTTCGGTTTGCTTAAAGGTGCTGGGAAATTTCGGGGAGGTAGAAATTACTGCAAACCCGAACCCGACCAAATAATTTGGGAAGTAAAAGCAGGAGACTGGGGTTCTGGAGGAGCCCTTCGACCTCGATCCAGAGTAAAACGTGACGTGCAAGGGCGGTCATTTCGGCAGTGGTGTCCACAGCTAGGCTCGCTGCCATTTTTATTTTTTAAGTGTAACAGGTGATACCTGCTGTCACCTGTGTCTCCTTTCGGGAGCCTCCCCAACCCTTGCCTACTATACCCTTATCGGGACCTCTGCCTTCTCAGGACTTTGAGGCAGTTATCGCAAGACATTTTAGACATCAGTCCTAGGTCTCCCTCCAACTTGCAGCACAGCCCCCCTCCCCCAAATAAAAGAGAAAATACAGTTTCTCTACAGCCAGTTACCTCATTCCGATCGCTCAATTTCCAAAAGATTATATGACCTTGCATCGGGTAATTATTTGAATAAATAGAACCTTAAGGGTCCGGGACTGGGAGCCCAGAGCTTGGTGGTTTGTGTTTTAACTGTCACAGGCAAATTGGCCAGAAGGATGCAGAATTAGGTTCTTTTTGCTGCTTTCTATTCTTCCTAAATGACTTTCTCGGGCTCTCTCCTTTCGCCATCTCTTCCCAG
Seq C2 exon
TGTCCACCCCTCTTGGCCAGGGCCGAGTCAACCAGCTCGGAGGAGTATTTATCAACGGCAGGCCTCTGCCCAACCATATCCGCCACAAGATAGTGGAGATGGCCCACCATGGCATTCGGCCTTGCGTCATTTCTCGCCAGCTTCGCGTGTCCCATGGTTGCGTCTCTAAGATCCTGTGCAGGTACCAGGAGACAGGCTCCATCCGACCTGGTGCCATCGGCGGCAGCAAACCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004872:ENSMUST00000087086:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (disopred):
C1=0.845 A=NA C2=0.215
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0029213=PAX=PU(57.9=92.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCACTCAAGGGACTCCTCT
R:
CAGAGGCCTGCCGTTGATAAA
Band lengths:
356-1534
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