MmuINT0118663 @ mm9
Intron Retention
Gene
ENSMUSG00000024193 | Phf1
Description
PHD finger protein 1 [Source:MGI Symbol;Acc:MGI:98647]
Coordinates
chr17:27071576-27072099:+
Coord C1 exon
chr17:27071576-27071671
Coord A exon
chr17:27071672-27071998
Coord C2 exon
chr17:27071999-27072099
Length
327 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
TCAACATTGTCCTTATTCAGCTT
3' ss Score
6.8
Exon sequences
Seq C1 exon
CTGCCCTCCCTGGGGAGGAGCTGCTCTGTTGTGTGTGTCGCTCTGAGACCGTGGTACCTGGGAACCGGCTGGTCAGCTGTGAGAAGTGTCGCCATG
Seq A exon
GTGAGAGGCCAGGATACTTAGGTGGTGCAGTCTGCCCTGGGTCTTCTGGGTTGCCACTAGCCCTGCCTTATAGCATGAGTTATGTCTCCTGTCCTGGCCAGTCTTCACCCTGTCACCACATCTCTCAGAACAGGGCGAGGGAGCCATAGATCAGGTGACCCAGGCCATGCAAAGCTGAGGGGCTTACATTACCTTTCTTAACCGTGCTTCCTTGGGCTAGGCCCTCAGCTGTGAGAAGCTTGTTGACTCACCTGCAGTGTCAGGATAACACACACAGCAGGACTTAGATGCACACAGTGGTCTACCCTCAACATTGTCCTTATTCAG
Seq C2 exon
CTTATCACCAGGACTGTCACGTTCCCAGGGCCCCGGCCCCTGGAGAAGGAGAGGGCGCATCCTGGGTATGCCGCCAGTGTGTCTTTGCAATCGCCACTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024193-Phf1:NM_009343:4
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:
PF150571=DUF4537=PD(15.8=27.3),PF0013017=C1_1=PU(68.3=84.8),PF0062824=PHD=PU(44.4=72.7)
A:
NA
C2:
PF0013017=C1_1=PD(29.3=35.3),PF0062824=PHD=PD(53.7=85.3)
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:
GGGAGGAGCTGCTCTGTTGT
R:
AGTGGCGATTGCAAAGACACA
Band lengths:
182-509
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: