MmuINT0115692 @ mm9
Intron Retention
Gene
ENSMUSG00000027168 | Pax6
Description
paired box gene 6 [Source:MGI Symbol;Acc:MGI:97490]
Coordinates
chr2:105532627-105533009:+
Coord C1 exon
chr2:105532627-105532777
Coord A exon
chr2:105532778-105532893
Coord C2 exon
chr2:105532894-105533009
Length
116 bp
Sequences
Splice sites
5' ss Seq
CTGGTAACT
5' ss Score
5.45
3' ss Seq
TCTTTTCTCTTCCTCTGCAGTCT
3' ss Score
10.88
Exon sequences
Seq C1 exon
GTATGGTTTTCTAATCGAAGGGCCAAATGGAGAAGAGAAGAGAAACTGAGGAACCAGAGAAGACAGGCCAGCAACACTCCTAGTCACATTCCTATCAGCAGCAGCTTCAGTACCAGTGTCTACCAGCCAATCCCACAGCCCACCACACCTG
Seq A exon
GTAACTTGAAATCCCACCTGCCAAGAACGGTTCTTAACCTTGCCTGCCCTTGACTTTCTCTTGCCTTGTAATGAATGACCTTGCCCTCTCTCTGTCTCTTTTCTCTTCCTCTGCAG
Seq C2 exon
TCTCCTCCTTCACATCAGGTTCCATGTTGGGCCGAACAGACACCGCCCTCACCAACACGTACAGTGCTTTGCCACCCATGCCCAGCTTCACCATGGCAAACAACCTGCCTATGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027168-Pax6:NM_013627:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.946 A=NA C2=0.992
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=21.6)
A:
NA
C2:
NO
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:
TCGAAGGGCCAAATGGAGAAG
R:
GGTTGTTTGCCATGGTGAAGC
Band lengths:
242-358
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: