MmuINT0118666 @ mm9
Intron Retention
Gene
ENSMUSG00000024193 | Phf1
Description
PHD finger protein 1 [Source:MGI Symbol;Acc:MGI:98647]
Coordinates
chr17:27072485-27072763:+
Coord C1 exon
chr17:27072485-27072580
Coord A exon
chr17:27072581-27072694
Coord C2 exon
chr17:27072695-27072763
Length
114 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CTGTCCTGGCCCATGTGCAGATT
3' ss Score
6.75
Exon sequences
Seq C1 exon
GTGGAACCTGAAAATGCTGCAGTGCCGGAGCTGCCTCCAGTGGTTCCATGAGGCCTGCACCCAGTGTCTGAGCAAGCCCCTCCTCTACGGAGACAG
Seq A exon
GTGAGACAGGACATGCACGCATGCTCGGGAGTCCACCTGTGCTCTCCCGCAGTCCTCTGCAGCCGGGGTCAGAGGGCTGAATGAGGTGCATCCTCTGTCCTGGCCCATGTGCAG
Seq C2 exon
ATTCTATGAATTTGAGTGCTGTGTGTGCCGGGGCGGCCCTGAGAAGGTCCGGAGGTTACAGCTTCGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024193-Phf1:NM_009343:7
Average complexity
IR-S
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=FE(58.2=100)
A:
NA
C2:
PF0062824=PHD=PD(25.5=58.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGAACCTGAAAATGCTGCA
R:
CGAAGCTGTAACCTCCGGAC
Band lengths:
162-276
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: