MmuINT0125891 @ mm9
Intron Retention
Gene
ENSMUSG00000029913 | Prdm5
Description
PR domain containing 5 [Source:MGI Symbol;Acc:MGI:1918029]
Coordinates
chr6:65805943-65807811:+
Coord C1 exon
chr6:65805943-65806117
Coord A exon
chr6:65806118-65807636
Coord C2 exon
chr6:65807637-65807811
Length
1519 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
CTGTGTTGTACATTGCACAGGTC
3' ss Score
6.42
Exon sequences
Seq C1 exon
GAAGGAGAAAATATTTTCTACTTGGCAGTTGATGATATAGAAACAGATACAGAGCTTTTGATTGGCTACCTGGACAGTGATGTGGAGGCAGAGGAGGAGGAGCAACAAGCTCTGACCATGACCAAAGAAGGCAAAGTTGACCACTCTAAGGGACAGTTGGCAGCTGGAAGTAAAG
Seq A exon
GTACTGCATCTTCGTTTGGTGATCTGAAGGAAGAGACATTGAAGAGGAAGGTAGCTTGAATTATTTGAATTATACTTGTGTGTTATGATGTGGTATTGTTAAAAGAGTGTTTGTCAAAACTATTCTTTTCCTCTGAATACCAGGAAAAGATTGTTTGGGGTAATTCCTGTAGGGTGGCCAGGGTAAGGCCACTCTGGTTCTTGTTGTCACTGTGGTATGATACACTGTCTGTCCCCTCCTGCACTGGTTCTGACAGTGGCCAGTAAGAAGGTCACTCAGGCTCTGAAGATTTCATCCCATGTACATGTGAGGAGGCCAGATCTGTAGGGTGGCCCTGCTGTGTCCTAGAGATCTGTCTTCTGAGATCTTCTGAGAAGCTGGACATTAGGGAAATCTTTCTAGTCTGGTCACAGGAGCTGGTAGGATTGTTAATTTGTCCTTGTCTGGGGATCAAAAACTTTAGGTGATCATAGATGATACCTGCAGTCTAGGAGAGGGATGACAGTTGGTTGTCAACTGGTGTGAAATAACCATTTATTTTTGGTCCCGTGTTTTATTCCTGCAGAAAACTTGAGGGAAAGTGCTGTGTTGTAGCACCATGTATCTTTGTCCATTTGGCCAAAAGGAATGCTTTTAAACAGTCAGAAGTTTCTTGTTCACAGTTCTGTCTGCAGTTCTCATTGAACTGAGGGACTAGCACACGTGGTGTCTGACTCCTTTCCTTATTTACAGAAGTTAAACATACAAGACACAAACGTGACCCCAGCAAGAGAAATGAAGACATCAGTCACATGTTTACCAGTGTAGTGTTTGATTACATGAATGTGGCACCTTAAATATGTGAATGACTGAGTTAGAAATGGGGAAAAGAGCCGTATGGGAGAGTGCACCTGAGATTTACTGCAGACATTGCACTTCACAGATGGAACACATATGGCTTTGGTATGCACCAGCTGCATCTTCAGGGTGGCATTATTAGTTAACTTTTTCATATTTAATATATTTTAACTCTAAAGATATGTAACTTTAATGGTACCCGGAAGAAGGTGGGTGGAGCTCTGTCAGTGGTGGGGAATAGGGTGCCTCACCTACCGCATCTGCGTAGACAGCAGTGTTTTCATGCTGTGCCTCTACTGTGAGATCCCCTTTGGCAGTTCACAGTAGTCTATGTCTGTTGGGTTCTTCTCCTGGTCAAGCTCAGAGTGAGCTGACGACGATCCATTTTCTAGGAAAAGACTTGCTTTGCAATTCAGAACTTATTGTTACTTCTGATCTGAAGCATTACCATTCAAAGGAAAACTGCAGATTGAATTTGATTTTGTAACTACTGTGAAGCATAATAAAATGATTTAAAAAAGTTTTTCTGATAACATTTTTGGTTTCTGTTTAATATGGACAATGTTAATGTTTGTTAGAGAAGACAAAAAAAATGGACTGTATCAGACACAACTAGTTTATTTTGAAGTGGGGGCCAAAGCTCGTTCCTTGCTTGTGAACTCCTGTGTTGTACATTGCACAG
Seq C2 exon
GTCACCTTGGCTGTGAAGAGGACTTTGCCTGTCCACAGTGTGAATCGAGCTTTCCCAGTGAGGAAGTCCTTACTGAGCACCTTCAGAGCTTGCACCAGAAGCCCACAGGGGAGAAAGAGTTCAAATGCGAGAACTGCGGGAAGAAATTCCCTGTGAGGCAGGCCTTGCAGAGACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029913-Prdm5:NM_027547:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.453 A=NA C2=0.141
Domain overlap (PFAM):
C1:
PF0085623=SET=FE(33.5=100)
A:
NA
C2:
PF089965=zf-DNA_Pol=PU(55.6=93.2),PF134651=zf-H2C2_2=WD(100=49.2),PF097235=Zn-ribbon_8=PU(57.6=32.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATATTTTCTACTTGGCAGTTGATGA
R:
CTGCCTCACAGGGAATTTCTTC
Band lengths:
327-1846
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: