MmuINT0115696 @ mm10
Intron Retention
Gene
ENSMUSG00000027168 | Pax6
Description
paired box 6 [Source:MGI Symbol;Acc:MGI:97490]
Coordinates
chr2:105680247-105683958:+
Coord C1 exon
chr2:105680247-105680307
Coord A exon
chr2:105680308-105683827
Coord C2 exon
chr2:105683828-105683958
Length
3520 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TCTCCTCGTCCTTTCCTCAGGTC
3' ss Score
11.96
Exon sequences
Seq C1 exon
AGCCCCGTATTCGAGCCCCGTGGGATCCGGAGGCTGCCAACCAGCTCCAGCATGCAGAACA
Seq A exon
GTAAGTGTCTCAGGTCTTTCTCTGGACTGTTGGGCTGGAGGCGTGCGGGCCGTGGGTTAGGGGAGCGTACTGAGTCTTGGGTCTTGAGGAGTCCAAGCCACTGGGAGAGAGGGAGGGAGGTGGCCTGGGATCTATCCGGGCAACACTGAGTGAGCGCCAAGTAGCCCGCGAGGAAAAGCTGAGAGACTTTTTTTGCTCTGCTAGGTTCTAGAAGGGCAGAGGCTGGGGCCCTTCAAAACTACTCGCCCGAGTTTTTGAAGCTGCGGTAGAGAAACCCCACCCCCCCACCCCAATCCTGTAACTCATACCCCCTCCCCGCCCCTGCCCGGGCTCTGACCCCAGAGAGAGGGGCTGGGCCGAGCAGGGCGGGGCGAAGCAAAGGCTTCTCCTGAGAAGAGAAGGAGGCCCCTTTGGGCTTGGCCAAGACTGTGCGATTCCTCCGACCCTGAGGGGTGGGGGGGGCTTCCCTCCCTTAGTCAATCTCTGGCCAGCTCCTCCCCTCCCCACCCTAGCTACCGGCCTAGAAGAGAAGGGGAGTGGAGCACCCAGGGCTGGTACCCTAGTGGGGAAGTAAACCTCACAGGGTTTACTGGAAAGGAGGGTTTCCTGGATCTGGGAAGAGAGTGGAAGCTGTGCGGGTCAGGAATTGGATAAACCTTGCACTAGCAAGAGCAACTGAGTGGGTTCTGGATGACCCAGGCCCCTGGTGCCTTTGACCAGGCTCCTTTGTGCCTCTCTTCTTACCTTTGCCCAGGTCCTTTGGGCCCCAACCTTTGTACTCAGCCAATGGTTGCTGGTATGTGATAGAGTTGAGCCACTGAAGCTAGGCCTGGGTAAAGGTGGAGATCTACACTGGCTACAACTATGCTTGGGAGTATGGAGAGGCTTGGGTCTTCTGTGGTTGTGGACTGGCAGAAGCTTAGAGAGACCAGCAGCTCTTGATGCCACAGGACGAGGGGCGCTAAGATCAGGAAAGTGAGCAAAGGTGTATTTGCGGCTGCATTTGTGCAGAACCTGTCAGATCCGTACCCTGGAGCTTGGACTCCTTAGCCTTAGGTTTTCAGGTGGGCCGAGGCGCTCAGTCGCGACCGTTTGCCGCTACACTATGGCCTGGCTGGCAGGCCCAGAGGGGTACGGGTCGCGGGTTGGCCTGTAGGCTTTGTGCCGCTGGTTCCCGGGTGTGCGCGAGGCGCGGAGCATCCAAATTGACACCATATGTTTTCGTATTAGAAGCTTTGCGGTCGAATTCTAGGCGCATAATCATCGCCACTGGGCGAGAACGCCAGCAGTCCCCAGGGAAGGGACACAATGATTGAGGCTTAACCTCTAAAGGGGAATTTAGAGCTATGTTTCTTCGCTGCCATTTCGTTGCTGGCAGAGGCGCCCTGGCCCCGTGTCTTTCAGACCAGCAAATCCGGGCTGCAGCTGTGGAGGTGCTGGGCACGTTAATTTTGCAATAAGGGATAAGGAAGGTCTATGAGGCCTTGCACACTCTGGCATCCGTAGACTGGGAATTACCCTGGCTTTGCTTTTGAAAAGTTTCTCTTCATTTCTCTGGGAAGGCCTTTCTTTTTCTGGGAAGCTTTCTTTTGCCCAGAGATGAGCCTCCATACCTGCATGGTAACTGAGATCTAGAAAGCCAAGGTAGATGATAAGAGAAAATTTAGGAGAAACCGGAAGCGCAAGGTAGGCCTTGCCCTGCTTAAGAAGCCCTCTCTTGCAATGTGCAATGTCCACTCTTGCACTGGCCCGGGACAGCCAGAGCCCAGATCTCTAAATGCCTGTCACTTTTCATCGAATTGAGGCCCCGCCCCCCCTCCGTGAGCTCTAACCCTCCTCCAGCCCCAAGCCTCAAGCTACCCTGAAAACGCAGCTCCCCTCGAAGGGGAGCCGAGTGCAGTTCATTCTCGTCTGAGTGATCTACAAATAGGGACGGAAAGGGTCGTTTTATCACGGTCCCGTTTGTCGTGACGATGCAATTTCCCGGAGCGGAGCACTGTCACAAAGTGACAAGGCTGCCACAAGCGCCCCGACTGATCTTTTCAATTAGCCTTCCATGCATGATCCGGAGCGACTTCCGCCTATTTCCAGAAATTAAGCTCAAACTTGACGTGCAGCTAGTTTTATTTTAAAGACAAATGTCAGAGAGGCTCATCATATTCCCCCCTCGTCTATATTTGGAGCTTATTTATTGCTAAGAAGCACAGGCTCCTGGAGTCAATTTATCAGGAGGCTCCAAGGAGAAGAGAGGAGAAGAGAGGAGACAAGAGAGGAGCTGAGAACCACATTTCCTTGAGAGGGCTTCTGTCTAGACACGGGGCTGCAGGTTGGAGATGTCCGAGGAAGTGGAAAGAGGGGACTGGTTTTTTTTTTTTTTCTATTCCTGTGGTTTCCGAGGAGGGTAAAATCATAGACGCGCTCCTTCCCTCTCGCCCTAGTCTCTACGACAAGACAATGGGATGAGGTTGTGAGACAAGAGTGGAAGGAAGGACCGGTGGCACTGTGATGTGGTCTTTTTCTTTTTCTGGTTTGGGTTTCTGTTAATATTTGTGTCCTTGGCTGAGGGGGAGGGCGGAGTTCAGCAGCGGAAGTAAAGCGAGTAGTGGCGGGTGGGAAGGCTCCAGGCTTCTGAGCACCACTTGGGGCAGGCGGATCACTGTGTGAGTGGGATTTCCAACTCTATGCCTGCTGTGGATGCACGGATTGGGGGGTCACTAGCGACAAATTTATCTTTCTGACTTTTTTCTATTCCACACGCGTGCGCGCACCACACACACACACACACACACACACACACACACACACACACACACACACGGTGCTATGTGCTGTGCACCTCTGCCAGAGTTAAATCACCATGCTAAGGTTTTATAACGTTCTGTAGAGCAGTGCAGGACTTGGGATTTGCAGTGCTGTTCCAACACTGCAGAGACTTCTGTGTGGACTCTGTGGTGACACTCAGAGGTGATGTAGGGAGAAGAATTTAAGAGCTTGACTTTTGCCCCTTGTGGGTTCCAAGAAGGGCTGGGGGTGCGTATGAAGGGGGCAATAGACTCAGGGATGATGGTATTGGGTGGATATGTTCCTGTGTATTCTCCCAGGTCTGACAACAGTCCAGTGGGCAGGTTCAAATTGTATTTGAGGCTGGGCTGCCCAGTATACTGCATGGCTGGTGGTTCTGTTATTGGGTGTTTTTTTTTTGTTTGTTTGTTTTTTTGTTTTTTTGTTTTTTAAAACCAGGACCTAATTGCTGAGGTTCACACAGGTTGGCAGGGAGCTGAGGTTGCATTGTGGTCTTTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTCTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTTCTTCTCCTTCTTTTTCTTCTTCTTCTTCCTCTTCTTCTTCTCTGCTCTCCTCTCCTCGTCCTTTCCTCAG
Seq C2 exon
GTCACAGCGGAGTGAATCAGCTTGGTGGTGTCTTTGTCAACGGGCGGCCACTGCCGGACTCCACCCGGCAGAAGATCGTAGAGCTAGCTCACAGCGGGGCCCGGCCGTGCGACATTTCCCGAATTCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027168:ENSMUST00000111086:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (disopred):
C1=1.000 A=NA C2=0.575
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(0.1=0.0)
A:
NA
C2:
PF0029213=PAX=PU(30.9=97.7)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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