MmuINT0125912 @ mm10
Intron Retention
Gene
ENSMUSG00000051977 | Prdm9
Description
PR domain containing 9 [Source:MGI Symbol;Acc:MGI:2384854]
Coordinates
chr17:15554688-15555358:-
Coord C1 exon
chr17:15555087-15555358
Coord A exon
chr17:15554756-15555086
Coord C2 exon
chr17:15554688-15554755
Length
331 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
TATTTCTTTCTGACACTCAGATT
3' ss Score
5.77
Exon sequences
Seq C1 exon
ATTGTGAGAAGTGCCAGAATTTCTTCATCGACAGTTGTCCCAACCATGGGCCTCCTTTATTTGTAAAAGACAGTATGGTGGACAGGGGGCATCCCAACCACTCAGTCCTCAGTCTGCCCCCTGGGCTAAGAATTAGTCCATCGGGCATCCCTGAAGCTGGACTTGGAGTATGGAATGAAGCATCTGATCTACCAGTCGGTCTGCACTTTGGCCCCTATGAGGGTCAGATCACAGAGGATGAAGAGGCAGCCAACAGTGGTTACTCCTGGCTG
Seq A exon
GTGAGAAATGCCTCCTTTTCCTTCATCTTCTGTCTCCCCATATCCTTTCTGTATTTCTGGTGTGACAAAGTAGAATATGGACAGGGACAACATGATTAATTTAGTGTACTGAATGGTCTTTGTTCAACATGGAAGTCCGGCTTCAAGGTCTGAAGGTGAGTAGGGGTGGAATGGTACAGAGACAAAGAAAACACATATGTACATGATGACTCAGAAGCCTCATGTGCGGTCGCTGTGAGTGGCTGAGTTCATAGCTCAGCACTGGTGAGTGTGAGGTGGCATGATTTCATTGTCATCCTGGAGCTTTAATGTATTTCTTTCTGACACTCAG
Seq C2 exon
ATTACCAAGGGAAGAAACTGCTATGAGTATGTGGATGGACAGGACGAGTCCCAAGCCAACTGGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000051977:ENSMUST00000147532:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.154 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0085623=SET=PU(24.4=23.1)
A:
NA
C2:
PF0085623=SET=FE(25.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGAGAAGTGCCAGAATTTCTTCA
R:
CATCCAGTTGGCTTGGGACTC
Band lengths:
336-667
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