MmuINT1026294 @ mm10
Intron Retention
Gene
ENSMUSG00000029706 | Pax4
Description
paired box 4 [Source:MGI Symbol;Acc:MGI:97488]
Coordinates
chr6:28443873-28444408:-
Coord C1 exon
chr6:28444339-28444408
Coord A exon
chr6:28443929-28444338
Coord C2 exon
chr6:28443873-28443928
Length
410 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATT
5' ss Score
5.95
3' ss Seq
GATTCACCCTCGCCTTATAGGTG
3' ss Score
9.41
Exon sequences
Seq C1 exon
GTTTGGTTTTCTAACAGAAGAGCCAAATGGCGCAGGCAAGAGAAGCTGAAATGGGAAGCACAGCTGCCAG
Seq A exon
GTGATTTCTGTGCACATCTATCCATCCATCCGTCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCTACATCTATCAACTGTCTGTCTGTCTGTCTATCCACCCATCCATCCATATTTACATAGCATTCCTCACGTGTCTTGCTTTGTGCTCGATCCTGGGCACACAGAGATCCTGTTCTTAAAGGCTGCTCTGACCCCAGAATCATCCCTTGGACTTAATCATTATTTCTAGTTTCCTAAGGCCCCGTTTTGGGAAGAAGACAGTCTAAGTTTGTGACATCTCCCTCTTCTAAACTCTGCAAGAAGTTGCAACCTTTCCTGGAACCTCTGTCTTTTACTACAACCCAGGTCCCCTTACCTATTTCTTCCTCTGAGTGGATTCACCCTCGCCTTATAG
Seq C2 exon
GTGCTTCCCAGGACCTGACAGTACCAAAAAATTCTCCAGGGATCATCTCTGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029706:ENSMUST00000031718:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.708 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=45.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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
- 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