MmuINT0115666 @ mm9
Intron Retention
Gene
ENSMUSG00000004872 | Pax3
Description
paired box gene 3 [Source:MGI Symbol;Acc:MGI:97487]
Coordinates
chr1:78097842-78100149:-
Coord C1 exon
chr1:78099903-78100149
Coord A exon
chr1:78099411-78099902
Coord C2 exon
chr1:78097842-78099410
Length
492 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGC
5' ss Score
7.31
3' ss Seq
CTGCGTGTGTTTCCTTACAGGTG
3' ss Score
12.84
Exon sequences
Seq C1 exon
GTAATGGGACTTCTGACCAACCACGGTGGGGTACCGCACCAGCCTCAGACCGACTATGCTCTCTCCCCTCTCACTGGGGGCCTGGAACCCACGACCACGGTGTCAGCCAGCTGCAGTCAGAGACTGGAACATATGAAGAATGTGGACAGTCTGCCCACATCTCAGCCCTATTGTCCCCCCACCTATAGCACCGCAGGCTACAGTATGGACCCTGTCACAGGCTACCAGTATGGGCAGTATGGACAAA
Seq A exon
GTAAGCCTTGGACGTTCTAGGGGGTAGTTCCTCCTGGAAGGGAGAGAGATCACCTCTTGCTTGAGAACGGGGAACTGGAGGCATGTTTAAGCCTTTCATCCCAGTATCATTTTTTTGTGGCAAAGACAGCTGATTGCTACAGCACAGGCTCCCTTGTGTAATTATTTGCTTAACTGATGTCAATAACATCTTGCAGTTATTAATTGCTGGGACGGAAAACCGGATTGTCAGTAGGTAAAACACAGAGGTTGGCCAAAATGAAATAACCTCTAGCATTAGAAACACATGTTCTTAATGAGGTCAGCGCCAGGATCATATGGGGATAAGCCCAGGACACAGAGTTGTGTCAAACTTGTCTCAGGAATAAAAATATTAGTCTCGATCCTTTGATACCGTGGTATTAAATATGACATTGTCAGCCTGTAGCTGATCTTGCCCCTAACTGTGAATTGTCCCAGCATGACCTAAAAAGCTGCGTGTGTTTCCTTACAG
Seq C2 exon
GTGCCTTTCATTATCTCAAGCCAGATATTGCATAAGTGAACTGTCCACTTGGAGCCCTGTTTCCGGCCTCCACAGACTAGACATGAAGAATCTTCTCAGAAACAAAACAATAAAAAAAATTTAAAAACAAACAAAAAATAAATGAAAAAAAATTCAGCTTTTGGGGGAGGTGGAGACAAAAGAGATTGATTTTCTTTCTCCAGTAGTTGCTTTCAGATTCTTTGAACATATTGGACAAAAGGCAGGGGAGACAAGGAAGACCCAGAGCTCTAAAATGCACCATTTTTAAGACAGTGATGTAACTGGCTACATATCAAAATGGCCCCAAATCTTTGTTGCTGATCAAAGAAGCTAAAACATTCCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGATTGATTTTCACGGGGTGGTTTGAGTAAGCAGAATGTTCCCATATATTGTAGTTGAATTCCTGAAAGTTAACAGGTTTGATGTCTAAGGCTGACCAAGTTTATGACATTCACACTGCTTATGTAGTGAATTGGGAATGGAGAAATCCTTGATTTTGACACACTGGAAACCGATATGAAAACCAACACCACCATTGTATAGGGCACTAGACTAGATGTGAAGGATCTCCCCAGTAAATTATTACCATACCTTCATTTGTAACCTAGTTATCAACCGATGTCCCTGACATGTCTTGTAAAAAGATGTGGGATAATGAGAAAAAAGTGTGTTATCTGCTGTGGGGATAGATGGATGTCATTTACTTCCCAAGTCACATTGATTTGGAGGCCAGTTGGTGGGGGGGGGGGAAGGGTATGATGTAGAGGAAGTGACACCCATCACATATCTGCTTCTCAGCGTGCAATACTGTGTACCTCACAGATGCTTTGGCAATGGCCAAGGTGATAGAAATGAAATCAGAACTATATTTTTGCAGGTGTTTTTATTTTTGCAGCCCATAACTCATCGTAGTAGAGTGCAGTGATGTTTGCTCGTTGCCAAACAACTCACATCCTGCTTGTTCCTTTTGTTCAGAGACCATGTCTGAGAATCAAGCTCTCTACAGAGATGGTGTTTACATTCGTCTCTTTTCTACAAAAGGCAGGGCTAGAACAGAAATGTCCACGTGGCTCTCATGTACTTTTAAATTATACAACGATACCCAATATTAAAGGATATAGGGAACAGGTTTACATACATTCATGTGGTGACATTTAGGATGTCAATAAATCTGTGTTTTGAAATGTTAAGAGAAAGATGAAGGTGGGCGGTGCTGTTATTTATTTCTTTCTATTCTTGGAACCATGAATGAGGTAGGCACAAATACATTCCCTTTAGATTTAAGAACAATGAGGTAGTGTGTTAGCAGGACTAGACATAGAACTGAGTTATTTTATACGTTGGGCAGGGTGATGGAACAGGAGACATAGTATCTTTGTGTTGCAGCCTCAACCAACAATGATGTGTTGTAAAAATGTCTTTCATGTAAAAAGTGCAGTAAATATTTACTATTTATAATGAATAAACAGTTAATGAAAATGTGCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004872-Pax3:NM_001159520:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (disopred):
C1=0.831 A=NA C2=0.182
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCTCAGCCCTATTGTCCCCC
R:
CCTTGTCTCCCCTGCCTTTTG
Band lengths:
345-837
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: