MmuINT0125909 @ mm10
Intron Retention
Gene
ENSMUSG00000051977 | Prdm9
Description
PR domain containing 9 [Source:MGI Symbol;Acc:MGI:2384854]
Coordinates
chr17:15557547-15559072:-
Coord C1 exon
chr17:15559023-15559072
Coord A exon
chr17:15557575-15559022
Coord C2 exon
chr17:15557547-15557574
Length
1448 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
CTTGTCTCTTCCTTATTCAGATA
3' ss Score
11.14
Exon sequences
Seq C1 exon
TCAGTCCTCCTTGGGTGCCTTTCCGGGTGAAGCACAGTAAACAGCAGAAG
Seq A exon
GTAAGTGCTTTCCAAATCCTACAGACAAGGAAACCTTCCTCATAGATCCAAACACAGGTAAGGAAAGGAGAAGGCTTAGAGTACCCTGGGAATTGCTACCTTCCCGGTCTCATCTACACAGTGTCTCTCAGCCTCCCGGTCATTTGAATTAATAAGAACATCACTCACTTGAGTGTTCCTACCTCAGTTTTTTTCTGCTATGTGAAAGTGAGAAATTCACTAATGTACTCTAAGGATAGTTTACAAATACAGAGGATTTTACTTTGAATGGCACACATAAAGGAGATATGATCCTCTCCTTCATAAAGACTCACTCTGATAAGAAACAGCAACTCTCGTCACTTAGAAGATTCAAGTTTAATAGCAAGGGATCCACAAATGAGACATGACTTAATCAGGCATGGTAGTGCTTGCCTGTAATTACATGAGAAGCAGAGTCCCAAGGAATACTGTGAGTTTGAGGCCAGCCTAGTCTACTTAAGGAGTTCCAGGTCTACCACAGGTATACAATGATATAATGAGTTTTGGAATGGGAAAAAGAAAAGGATGTAAGCGTTCATATAGGCAAATAATTTCCATAGAAATATCATCTGTCGGAAAGACTGAGAGAAGCTAGTAATCTCACACTAGTATTATATTCAGTTGTGGGTATTCTAAATAGAATTATTATGTCTGGGTGGTTGGAGAGAGGGCTCAGTGGTTAATAGCATTTCTTGTTCTTCCAAAGGTCCTGAGCTGTACAGTTCAAAACTACCCTTTAACTCCAACTCCAAGAGATTGAATGCCCTTGTCTTACTCTGACAGAACCTGTGCACCACCCCCTCACACACACAAATAGAAATGAAAATAAATCTTTTAAAAATGAACAATTAGCATGTATACAAACTTATGAGTGAAAAAATTATTGAATTTTTCTGGAAAATTAGTACAAGAATTAATCTAATTCCAGAGTCATCCTAAGCATTATGCTCAGATCTGTAGTTTGAGCACTTGAAAGGCTGAGGTAGGAGGAATCCTGTGAGTTTGAGGCCAGCCTCTATCATGAGACCCCCATCTCAAACAAGCAACCTAATTCTAGAATCAACTATTTCCAGAATGCCAATTTACAATTTTATCATTACTTCGTTAGTTGTAGAGGTACATTTCTGCCGCCATCTCTTCATTTTCTTCCCAGAGACACTGCTCTGCTCTCACTTCCCTTTACAGATGTGTTTTATCAACTTTGTTTTCTACATTTCTCATCTGATCAATATTTCCTACTTTACGGATATACCCTCTTTCTCTCTGTAAGCCCTATCTTCTTCATTGCAAACTTTGTTGACCTTCCAGCTAGCCTTCCCAAGTATCTACCTTCCTCAAGCCTGAAAGAAGCCTGAAGGGAGAAAGCCTAGCAGATGGCCTCTTGCCCTGGATTCATTTAAGTTCTTCCTTGTCTCTTCCTTATTCAG
Seq C2 exon
ATACTCTACACATTAACTAAAGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000051977:ENSMUST00000147532:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.353 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
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
- 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