MmuINT0125892 @ mm9
Intron Retention
Gene
ENSMUSG00000029913 | Prdm5
Description
PR domain containing 5 [Source:MGI Symbol;Acc:MGI:1918029]
Coordinates
chr6:65807637-65809472:+
Coord C1 exon
chr6:65807637-65807811
Coord A exon
chr6:65807812-65809350
Coord C2 exon
chr6:65809351-65809472
Length
1539 bp
Sequences
Splice sites
5' ss Seq
ACAGTGCGT
5' ss Score
5.66
3' ss Seq
CCTTGCTGCTTGTCTTATAGTTT
3' ss Score
8.36
Exon sequences
Seq C1 exon
GTCACCTTGGCTGTGAAGAGGACTTTGCCTGTCCACAGTGTGAATCGAGCTTTCCCAGTGAGGAAGTCCTTACTGAGCACCTTCAGAGCTTGCACCAGAAGCCCACAGGGGAGAAAGAGTTCAAATGCGAGAACTGCGGGAAGAAATTCCCTGTGAGGCAGGCCTTGCAGAGACA
Seq A exon
GTGCGTATGCTCAGGGTGGTTCAGCTTGTGTTTGAACAGTCAGATTATTTACTGTGCTTGCTATGTATATCTGTGTCTGTGAGCATGCGCCAAAGCATATGTGGGAAAGTGGCAGGTAGCCTACTGTGCTATGAGCTCATCTTTTCCGAGAGGAGCGTGCTGAGTTTCAAATGCTCTGAGCATGAGGTTTACAGGTCAACATCATTCCTGCTAAGCCCTTTTGGTGCATTTCATACTTGCCATTAAATATCATGCTTAATGGTTTAATAATGGTTTATGTATGCATAATTTAGCCAGTGCTTGAGGTTATTCACCAAGTTTCACTTATTTGCCCTCTAATTTGCTTAAAACTGTTTAACTGATAAAGAATTCAGTGTATTGATAATGGAAGGCTGGGAAGCAGCACCTGTTTCCCAGTGAGTTGGAAGACTAGTTTGAAGATGAGTGGGTCAGTGTGTGGCAGTGAGGTGAAGTACATGAATTACCCATTACCTTATTCCTAATCACTTGTGTCTACAACATAAAATTAGCTTCTATTTTAACATTTTGTAAGATCAGAGCTACCAAAAGTGAGAGAATATACAGACTCCAAAATTCTACACTTAGCAAACTGTCACCTTACATGAGTAAAACAGCTTCCAGAATATTTAATGTTTCCATTTTGTTGTGTTTAACTCCAAAGTATGCCATTTCATTCCTTTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATTATCTATCAATCTATCTATCTATCTATCATCTATCTACCTACCTACCTATCATCTATCTGTCATTTATAGAGATGACATTTCTATATATTATATGCATCAGGTTTTGCTTATGAAATATAAAAATAATTTTATTTACAAGTAACAAATCTTTCAAAAATTGATACCTTTAGGATGACTTAAACATTTAGGGATTTTTACTAACTTCTTCAAATAAAGCCAAGCAAAAGTTATAATACTTTTTAACAAGTTAACTTTAGCTTGCATTTTAGTCAGCTTTTATATGTATTTATTGCACTGTCAGATTTTGAACTATATCTTAGAGCTAATAGGCTACCATTAAAATGTAGAAGACCACACAGGGCAGCACAAGGCTGGGAGCATATCCTGGCACTCTGGCTTCTTCACCCGTTCTCCTCACTGCACTTTTCTGCACAGCCAGAAGCAGCTTGAAAAATTCTTCATCGAGTGTTCAGTGTGCTCTTTGCAATTCTCTTTTCAGTTCAGCACTGAGGTTTAGCGTCTGGTTATGAAATGGCTTTCACAAGTCTGCAGGTCATTTTCTCGTGCATAATTCATGCTTGGAGCAAGTCAGCACTGCACTAAGTAAACTGGAGGATTTGGATACATCTTTCTTACCAACATAATTAATGCATGAAATGACCTCCAGACTCCTGCAGGAAGGAAGTCCGGGGAGGCATGGGTTGCAGAAACCTTGTGTGATGTTTGCGTGTGTAGGCATACCTTCATCATTTCTTCTGCCGCCTTGCTGCTTGTCTTATAG
Seq C2 exon
TTTTGAGCAGCACCGGAAGGCTTGCCGAGGGGAGGCCAGGTTTGTGTGCAAAGCCGACAGCTGCGGGAAGAGGCTGAAAAGCAAGGATGCCCTGCGAAGGCACCAGGAAAATGTCCACACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029913-Prdm5:NM_027547:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.141 A=NA C2=0.214
Domain overlap (PFAM):
C1:
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)
A:
NA
C2:
PF089965=zf-DNA_Pol=FE(41.4=100),PF097235=Zn-ribbon_8=PD(39.4=31.0),PF0009621=zf-C2H2=WD(100=61.9)
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:
GTCACCTTGGCTGTGAAGAGG
R:
TGTGGACATTTTCCTGGTGCC
Band lengths:
294-1833
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: