MmuINT0115702 @ mm10
Intron Retention
Gene
ENSMUSG00000027168 | Pax6
Description
paired box 6 [Source:MGI Symbol;Acc:MGI:97490]
Coordinates
chr2:105692194-105692620:+
Coord C1 exon
chr2:105692194-105692276
Coord A exon
chr2:105692277-105692469
Coord C2 exon
chr2:105692470-105692620
Length
193 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCT
5' ss Score
8.16
3' ss Seq
CCTGTTCTGTGCATTTCCAGGTA
3' ss Score
11.27
Exon sequences
Seq C1 exon
AGTTTGAGAGGACCCATTATCCAGATGTGTTTGCCCGGGAAAGACTAGCAGCCAAAATAGATCTACCTGAAGCAAGAATACAG
Seq A exon
GTACCTAGGGACCATGTGGTTTTTATGCACTGGGATGCTTATATTTTGCCTTGGCTGTATACCAGTCACTGATATAATCATGGTCAGGTTTGCAAAGACTCCCTTGTTCTAGGGTAAGGGTGGGGATGGAGGGCTTTTTGTTTGTGGCCGAGTGGTAGCAAGCATAGGGCTAACCTGTTCTGTGCATTTCCAG
Seq C2 exon
GTATGGTTTTCTAATCGAAGGGCCAAATGGAGAAGAGAAGAGAAACTGAGGAACCAGAGAAGACAGGCCAGCAACACTCCTAGTCACATTCCTATCAGCAGCAGCTTCAGTACCAGTGTCTACCAGCCAATCCCACAGCCCACCACACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027168:ENSMUST00000111086:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.873 A=NA C2=0.965
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(47.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=21.6)
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:
AGTTTGAGAGGACCCATTATCCAGA
R:
CAGGTGTGGTGGGCTGTG
Band lengths:
234-427
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