MmuINT0115678 @ mm10
Intron Retention
Gene
ENSMUSG00000029706 | Pax4
Description
paired box 4 [Source:MGI Symbol;Acc:MGI:97488]
Coordinates
chr6:28444804-28445238:-
Coord C1 exon
chr6:28445113-28445238
Coord A exon
chr6:28444887-28445112
Coord C2 exon
chr6:28444804-28444886
Length
226 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCTG
5' ss Score
4.05
3' ss Seq
GAGAGCCTCTGTCTCTACAGAGT
3' ss Score
6.43
Exon sequences
Seq C1 exon
CTGTGTTGGCTCCAGTTCTTCCCAGTCCCCACAGTAACTGTGGGGCTCCCCGAGGTCCCCACCCAGGAACCAGCCACAGGAATCGGACTATCTTCTCCCCGGGACAAGCCGAGGCACTGGAGAAAG
Seq A exon
GTGCTGGACTTGGGTAGACAGTGGGAAAGATGCTGCTGGTATGGTGGCAAGGCAACAAACAGTCTTGAGACTTATGGGTGAAGGCTGACAGGGTCCAGGCTGTGGGTGGCTTGACCTTGGGAAGACGGGTTATTTAGGCTTTTAAGAAGTAGGGAGTGGGGACTGACAAGGAGACCATTCCTTACTCCTTCCCTTACCCTCACTGTGAGAGCCTCTGTCTCTACAG
Seq C2 exon
AGTTTCAGCGTGGGCAGTATCCAGATTCAGTGGCCCGTGGGAAGCTGGCTGCTGCCACCTCTCTGCCTGAAGACACGGTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029706:ENSMUST00000031718:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=1.000 A=NA C2=0.616
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(29.8=39.5)
A:
NA
C2:
PF0004624=Homeobox=FE(47.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGGCTCCAGTTCTTCCCAG
R:
CTCACCGTGTCTTCAGGCAGA
Band lengths:
204-430
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