MmuINT0118665 @ mm10
Intron Retention
Gene
ENSMUSG00000024193 | Phf1
Description
PHD finger protein 1 [Source:MGI Symbol;Acc:MGI:98647]
Coordinates
chr17:26935249-26935635:+
Coord C1 exon
chr17:26935249-26935397
Coord A exon
chr17:26935398-26935539
Coord C2 exon
chr17:26935540-26935635
Length
142 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
AAGCGCTGTCTCCCCTCCAGGTG
3' ss Score
9.8
Exon sequences
Seq C1 exon
AGGGGAGGCGCACTGAAGAAAGGTCCCTATGCCCGGGCCATGCTGGGCATGAAGCTCTCCCTGCCATACGGATTAAAAGGGCTGGACTGGGATGCTGGACATTTGAGCAACAGACAGCAGAGCTACTGCTACTGTGGAGGCCCTGGAGA
Seq A exon
GTGAGTGGAGAGGGTGTTGTCAAGCTATGGGATGGGGGTTGTTGTGGTGGCAGAGCCCGGGAAAATGGGTGAACAGGGGGCGAGGGGGCCCTGTGGTTTCAAGAAGGCTGTCTGAGGGCCACAAGCGCTGTCTCCCCTCCAG
Seq C2 exon
GTGGAACCTGAAAATGCTGCAGTGCCGGAGCTGCCTCCAGTGGTTCCATGAGGCCTGCACCCAGTGTCTGAGCAAGCCCCTCCTCTACGGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024193:ENSMUST00000073724:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062824=PHD=PU(14.5=16.0)
A:
NA
C2:
PF0062824=PHD=FE(58.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGGCGCACTGAAGAAAGG
R:
GTAGAGGAGGGGCTTGCTCAG
Band lengths:
234-376
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