MmuINT0125910 @ mm10
Intron Retention
Gene
ENSMUSG00000051977 | Prdm9
Description
PR domain containing 9 [Source:MGI Symbol;Acc:MGI:2384854]
Coordinates
chr17:15555566-15557457:-
Coord C1 exon
chr17:15557301-15557457
Coord A exon
chr17:15555668-15557300
Coord C2 exon
chr17:15555566-15555667
Length
1633 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGA
5' ss Score
5.11
3' ss Seq
CCCTTTGTTCTCCACTCCAGAAC
3' ss Score
10.6
Exon sequences
Seq C1 exon
GAATCATCTAGAATGCCATTTAGTGGTGAATCTAATGTGAAGGAAGGGTCTGGAATAGAAAATTTGCTGAATACAAGTGGCTCAGAACACGTCCAGAAACCAGTGTCCTCCCTTGAAGAAGGAAATACCTCTGGACAGCACTCTGGGAAAAAACTGA
Seq A exon
GTAAGAGTAAATAATTTGGGAACTTTAATCCCTCTCGGAAGGTTAATGAGAATAGTCTGGGATGGTCAGTGTAGTAACTTCAGAAAGTTCTGAACTTGGTCTTGTCTAAGCTGTGGCATTGATAGTGGGCATGCTATTAAGTAATATGTCAGAACACCTACTTTAAATGCATAAATTTGGGTTGTTACTCACATGGAGGTACTGGGACTTGGGCAATCTTACAAACTCTGCAACCTTGTGAACATTAATATGTGGAAATAAGGATATGGTAGGTAGCTCTAATGTTGCTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTCTTTCCCTTTCCCTTTCCCTTTCCCTTCTTTCCCTTTCCCTTTCCCTTCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTGATTTTTCGAGACAGGGTTTCTCTGTATAGCCCTGGCTGCCCTGGAGCTCACTTTGTAGACCAGGCTGCCTCGAACTCAGAAATCCACCTGCCCCTGCCTCCAGAGTGCTGGGATTAAAGGCGTGTGCCACCATGCCTGGCCTCTAATGTTGCTTTCAAACAGCAAGTGAAGCATAAAGCAACTGATCCAATAAATCTCTGTGGCAATAGAAACCAAATACTCTCAATGCTGTTTGCCCAGGTCTTTGTTCAATGCCTAATTGCAGTGGGCCCTTAATTAATATTTTATAAATGGATCAACATGTCAATGAACTATTTTTAAGTAGAAAATGTGAGCAAGTAGAAATTAAACCTGAAGAGTCAGAAATTAAAATTAGATTAGACATCTGTTGTCAGTTGAATATGGGATCTTAGCTTCTTTAAACAAAAAGTTAAAAGGAGAGCATATGGCAGTAAATTTCACATTTTGTTTTAAAACATTTTAAAGTAAATTTTTTATTTTTTTGTTTGTTTGTTTGTTTGTTTTTCGAGACAGGATTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCATGAGCCACCACGCCTGGCAATTTTTTAGTTTTTTAAAGATTTATTTTTATATGCATATGAATGTCTGCCTCCATGTATGTATGTGTACCATGTACATGCCTGATGCCTGCAGAGATGGAATGAGAGTATTTGATTAGCTAAAACTGGAGTTACAGATGGTTTAAAGCCATGGTGTGAGTGCTAAGAACCAAACCCAGGTCCTCTAAACATACACTTTAACTGCTGGGCTATATTCCCAGGCCCAGATTTTAGATTTTTATGAAGAAATGGGGATAAATGCTTGAGATTCACACACTTTAAGTCCCCTTTGTTCTCCACTCCAG
Seq C2 exon
AACTTAGGAAAAAGAACGTTGAAGTGAAAATGTACAGGCTGCGAGAGAGAAAGGGCCTTGCCTATGAGGAGGTCAGCGAGCCTCAGGATGATGACTATCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000051977:ENSMUST00000147532:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.952 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF095145=SSXRD=PU(0.1=0.0)
A:
NA
C2:
PF095145=SSXRD=WD(100=94.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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:
CCATTTAGTGGTGAATCTAATGTGA
R:
AGTCATCATCCTGAGGCTCGC
Band lengths:
238-1871
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