DreINT0113223 @ danRer10
Intron Retention
Gene
ENSDARG00000057439 | phf1
Description
PHD finger protein 1 [Source:ZFIN;Acc:ZDB-GENE-100922-277]
Coordinates
chr16:45469716-45469963:+
Coord C1 exon
chr16:45469716-45469811
Coord A exon
chr16:45469812-45469894
Coord C2 exon
chr16:45469895-45469963
Length
83 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGG
5' ss Score
8.99
3' ss Seq
GTCTCCTCTTCACCTTTCAGCTT
3' ss Score
10.3
Exon sequences
Seq C1 exon
GTGGAATCTAAAGATGCTGCAGTGTGGCAGTTGTGGACAGTGGTTTCATGAAGCCTGCACTCAGTGCCTGAGCAAACCTCTTCTGTATGGAGATCG
Seq A exon
GTGAGGCTGTTATTCAGCACAGACTGTTACTAAACTCATTGAGTGTAAAGCTTTTTCACAATCGTCTCCTCTTCACCTTTCAG
Seq C2 exon
CTTTTATCAGTTCCAGTGCTCCGTCTGCAGCAATGGAGCAGAGAGCGTCCAGAGGCTTCCCATGACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000057439:ENSDART00000134471:7
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=FE(60.4=100)
A:
NA
C2:
PF0062824=PHD=PD(22.6=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTAAAGATGCTGCAGTGTGGC
R:
CAGGTCATGGGAAGCCTCTGG
Band lengths:
159-242
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]