MmuINT1027366 @ mm10
Intron Retention
Gene
ENSMUSG00000051977 | Prdm9
Description
PR domain containing 9 [Source:MGI Symbol;Acc:MGI:2384854]
Coordinates
chr17:15563221-15564340:-
Coord C1 exon
chr17:15564236-15564340
Coord A exon
chr17:15563332-15564235
Coord C2 exon
chr17:15563221-15563331
Length
904 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGA
5' ss Score
3.61
3' ss Seq
AGTTACCTCTTCATCCATAGGAC
3' ss Score
8.98
Exon sequences
Seq C1 exon
CTCCTCAGAGGGACGAACGCCGGCGGTGGCCTCAGAGCCGCGGGATTCTGGACCATGAGTGCAGGCGAAACCTTCAGGACCAGCGAGGCTTTCTAGGCTCAGCCC
Seq A exon
GTGAGACCCCATATCCCCTAAATTAGATTCGGACCCCCTCAGCGTGACACGCGCGCGCGCGCTCACACGCACACACCCGGTCACCTCAGCTTCTCGGGAACTCCAAACGCCCTTTGGCTGAGTGAGGTCCCAAATGCACTTGTGCGGAACCAACCCAGCCTCTGCCTGAGGAACCTGGGTAGCTCGCCTCAGAGAGACTAAGTTTCCAGACAGGAAACCTGGACTCTCAGCGTAGAGACTCTCCTAAGCCCCAAAGACCCCAGACGCCCTCGGTCTCGAGGACCTGTCTGTCACTCCAGATTGGCTTCCAGAGATCCTAAATGCTCTCGTCCCGCAGGACCCTAAATACCTCCGACGTGACAAATCCCAACTCTTCGTGACATAATCGTCAAATCTCGTCAGACTGCGAGTCTCCAAACCTTATTTCACAGCCTGAAAGACTCCTCTAGCCTACGAACCCAATTCCTTCAATCTGATGCACCCCACTCCTCAGCCCGAGGTCCCCAAAGTTAAAATCTCAGCCAGAGCGTTCCTACATTTTCACCAGAGGGACTTCAATCCCTTGTACTCGGGATTCCCGAATCCATTTACCTGAAAACATCTTTCAGACCCTGGCTGACTCCTTGGTCCAGATGAAGAGCAAGTGGGAATGGGGTGGGGGGGGACACCGGTTGGCGGGAGGAATCTTCCTTCCTTGCTGTCGCAGGTCCTGACCCGGACGGAGGGTCGGTGCCTAGGTTTAGGGCTCAGTCCAGAATCCTTGCTCCTGCACCAGAGTACTAGACCTCGGAGTCCGAAGAAGCTGCCTGTGTTGGCTGCATGGATTCCCAGCCCCTAGCTCCTTCCCATGTGCTGGTGGGCATCTCTGATCGCCTAAGGCCCTTAGTTACCTCTTCATCCATAG
Seq C2 exon
GACCATAGGACCCTGGACCTCTCCAGTGAAATGTCCTGCACCATGAACACCAACAAGCTGGAAGAAAATAGTCCTGAAGAAGATACAGGGAAATTCGAGTGGAAACCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000051977:ENSMUST00000147532:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.815
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
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:
CTCCTCAGAGGGACGAACGC
R:
TGGGTTTCCACTCGAATTTCCC
Band lengths:
214-1118
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