RnoINT0110311 @ rn6
Intron Retention
Gene
ENSRNOG00000000480 | Phf1
Description
PHD finger protein 1 [Source:RGD Symbol;Acc:1303205]
Coordinates
chr20:5529126-5529511:+
Coord C1 exon
chr20:5529126-5529274
Coord A exon
chr20:5529275-5529415
Coord C2 exon
chr20:5529416-5529511
Length
141 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
GGCGCTGTCTTCCCCTTGAGGTG
3' ss Score
2.7
Exon sequences
Seq C1 exon
AGGGGAGGTGCCCTGAAGAAGGGTCCCTATGCCCGGGCCATGCTGGGCATGAAACTCTCCCTGCCGTACGGTCTGAAAGGGCTGGACTGGGACGCCGGACATCTGAGCAACAGGCAGCAGAGCTACTGTTACTGCGGGGGCCCGGGGGA
Seq A exon
GTAAGTGAAGGAAGAGCAGGGCCAGCCACGGCATGGGTGTTTTGTGGTGGTAGAGCCCAGGACAGAGGGGAGCGAAGAGGGTGAGGGGGGGCCCTGTGGTTTGAAGAAGGCTGAGGGCCATGGCGCTGTCTTCCCCTTGAG
Seq C2 exon
GTGGAACCTGAAAATGCTGCAATGCCGGAGCTGCCTCCAGTGGTTCCATGAGGCCTGCACCCAGTGTCTGAGCAAGCCCCTCCTTTACGGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000480:ENSRNOT00000059548:6
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(14.5=16.0)
A:
NA
C2:
PF0062824=PHD=FE(58.2=100)
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:
GGAGGTGCCCTGAAGAAGG
R:
GTAAAGGAGGGGCTTGCTCAG
Band lengths:
234-375
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]