MmuINT0118661 @ mm10
Intron Retention
Gene
ENSMUSG00000024193 | Phf1
Description
PHD finger protein 1 [Source:MGI Symbol;Acc:MGI:98647]
Coordinates
chr17:26934194-26934535:+
Coord C1 exon
chr17:26934194-26934368
Coord A exon
chr17:26934369-26934453
Coord C2 exon
chr17:26934454-26934535
Length
85 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TCACTGGGCACCCATTCCAGGTG
3' ss Score
7.38
Exon sequences
Seq C1 exon
GCCCCCCCAGGATGCAATGGCGCAGCTCCCCCGGCTGAGCCGTTTGGGTGCCCCCTCTCTCTGGGATCCAGCTTCCCCTGCTCCCACCTCAGGCCCCAGACCTCGGCTTTGGGAAGGCCAAGATGTGCTGGCCAGATGGACTGATGGGCTGCTGTACTTGGGTACCATCAAAAAG
Seq A exon
GTAAGACCCACCTCTGATCTCACTGCCTTCCCAGTCTCCAGTCAGTTCTCATTCCCATTTTAGCATCACTGGGCACCCATTCCAG
Seq C2 exon
GTGGACAGTGCTCGAGAGGTGTGTCTGGTCCAGTTTGAGGACGATTCCCAGTTTCTGGTTCTATGGAAGGATATCAGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024193:ENSMUST00000073724:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.226 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF150571=DUF4537=PU(33.3=35.8)
A:
NA
C2:
PF150571=DUF4537=FE(47.4=100)
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:
GGTGCCCCCTCTCTCTGG
R:
TCAAACTGGACCAGACACACC
Band lengths:
167-252
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