MmuINT0115699 @ mm10
Intron Retention
Gene
ENSMUSG00000027168 | Pax6
Description
paired box 6 [Source:MGI Symbol;Acc:MGI:97490]
Coordinates
chr2:105684887-105685943:+
Coord C1 exon
chr2:105684887-105685102
Coord A exon
chr2:105685103-105685777
Coord C2 exon
chr2:105685778-105685943
Length
675 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
CCATTTGGTTTGATTTGCAGGTG
3' ss Score
9.83
Exon sequences
Seq C1 exon
GTATCCAACGGTTGTGTGAGTAAAATTCTGGGCAGGTATTACGAGACTGGCTCCATCAGACCCAGGGCAATCGGAGGGAGTAAGCCAAGAGTGGCGACTCCAGAAGTTGTAAGCAAAATAGCCCAGTATAAACGGGAGTGCCCTTCCATCTTTGCTTGGGAAATCCGAGACAGATTATTATCCGAGGGGGTCTGTACCAACGATAACATACCCAGT
Seq A exon
GTAAGTTTATTGTGAACATCGTGTGTCTACCTTGCCCCAAGGCCCATCTCTGGCGCGTCTTTATCTCCTCCTGCTCTTTTCTCTCCCCAGGCCTTGCCATCTCTCTCCCTCTCTTCCCTGATTTGTCTCCAGGGTACCTGGGGGTATGGAGAGGTGGGCTTTGACTTTTTGACCATCTGGAAAATGGGGGTGAAGTGTGAGGAGTAGTTCCCTTCATTTGGATACCACAGACCAGGGGTCAAAGGAACTAGGGAAAGGCACTTGGAAATGAAAATGAAAACCAGATTCTAAATTCCCCTCAAAGCATTTTCCTGAAGCTTCTTTCAGGCAACATGCATCCATTTCTGCTCTCCGATAAAGTAGATCTCTAAAGTAAGTCTTTTATCACTGAGTCTTGGATCAAAGCGGAGCAGCCCAGTGAGCGGTTATTCGTGATATCTACAGAGGTGAAGGACTGCTCCCTCCTTTACACCCAACTTCATTTCCAGGAACAAAATGATAGCTGCCATTCTTTCCACAAAATAAGTTAAAAATCCACAGACTGTTCCAGGATGGCTGGGAGCTTTTGCATGTGTAGTGGGGTCATTCTTTAAAGCTTGGGAGAGCTGAGATGGGGACCTAAGATGGGGTGACTACGTGTCTTTCGGAGACACTACCATTTGGTTTGATTTGCAG
Seq C2 exon
GTGTCATCAATAAACAGAGTTCTTCGCAACCTGGCTAGCGAAAAGCAACAGATGGGCGCAGACGGCATGTATGATAAACTAAGGATGTTGAACGGGCAGACCGGAAGCTGGGGCACACGCCCTGGTTGGTATCCCGGGACTTCAGTACCAGGGCAACCCACGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027168:ENSMUST00000111086:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=NA C2=0.784
Domain overlap (PFAM):
C1:
PF0029213=PAX=FE(51.1=100)
A:
NA
C2:
PF0029213=PAX=PD(5.8=14.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAGGTATTACGAGACTGGC
R:
GTTGCCCTGGTACTGAAGTCC
Band lengths:
343-1018
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