DreINT0113220 @ danRer10
Intron Retention
Gene
ENSDARG00000057439 | phf1
Description
PHD finger protein 1 [Source:ZFIN;Acc:ZDB-GENE-100922-277]
Coordinates
chr16:45463997-45464269:+
Coord C1 exon
chr16:45463997-45464083
Coord A exon
chr16:45464084-45464174
Coord C2 exon
chr16:45464175-45464269
Length
91 bp
Sequences
Splice sites
5' ss Seq
ACGGTATTG
5' ss Score
4.64
3' ss Seq
GCATTTGTTTGTTTCCTCAGGTT
3' ss Score
10.3
Exon sequences
Seq C1 exon
TCTCTTCAGGAGGAGAGGAGGTTTGCTGTATCTGTGATTCGCCACCTCTTAAAGAACCTCTCGTAAACTGCCTCAAATGTCGCCACG
Seq A exon
GTATTGAAAATACAACTATTTTGATTCTTTCTATTTGTCTTGGATTTAATGTGTATGCTTTGTACATGAATGCATTTGTTTGTTTCCTCAG
Seq C2 exon
GTTATCATCCAGAGTGCCATACCCCGTCCATAGAGCCTGAAGTCGACCCCAACAGCTGGATTTGTCGCCAATGTGTCTTCGCAGTTGCAACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000057439:ENSDART00000134471:4
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(44.0=73.3)
A:
NA
C2:
PF0062824=PHD=PD(54.0=84.4)
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:
TCAGGAGGAGAGGAGGTTTGC
R:
TTGGTTGCAACTGCGAAGACA
Band lengths:
176-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]