MmuINT0125892 @ mm10
Intron Retention
Gene
ENSMUSG00000029913 | Prdm5
Description
PR domain containing 5 [Source:MGI Symbol;Acc:MGI:1918029]
Coordinates
chr6:65857643-65859478:+
Coord C1 exon
chr6:65857643-65857817
Coord A exon
chr6:65857818-65859356
Coord C2 exon
chr6:65859357-65859478
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:ENSMUST00000031976:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.140 A=NA C2=0.187
Domain overlap (PFAM):
C1:
PF134651=zf-H2C2_2=WD(100=49.2)
A:
NA
C2:
PF0009621=zf-C2H2=WD(100=61.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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
- 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