RnoINT0110312 @ rn6
Intron Retention
Gene
ENSRNOG00000000480 | Phf1
Description
PHD finger protein 1 [Source:RGD Symbol;Acc:1303205]
Coordinates
chr20:5529416-5529708:+
Coord C1 exon
chr20:5529416-5529511
Coord A exon
chr20:5529512-5529639
Coord C2 exon
chr20:5529640-5529708
Length
128 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CTGTCCTGACCCATATACAGATT
3' ss Score
5.82
Exon sequences
Seq C1 exon
GTGGAACCTGAAAATGCTGCAATGCCGGAGCTGCCTCCAGTGGTTCCATGAGGCCTGCACCCAGTGTCTGAGCAAGCCCCTCCTTTACGGAGACAG
Seq A exon
GTGAGATCCAGGGAGACTGCACAGGAGCCTGGGGTGCTCTCTCTCCCGCGCTCCCGACTGACTAGTTAGCCCTCTGCAGCTCGTACTGGAGGGTTGAGTGAGGTCCCTCTGTCCTGACCCATATACAG
Seq C2 exon
ATTCTATGAATTTGAATGCTGTGTGTGCCGGGGCGGCCCTGAGAAAGTACGGAGGTTACAGCTTCGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000480:ENSRNOT00000059548:7
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(58.2=100)
A:
NA
C2:
PF0062824=PHD=PD(25.5=58.3)
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:
GTGGAACCTGAAAATGCTGCA
R:
CGAAGCTGTAACCTCCGTACT
Band lengths:
162-290
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]