RnoINT0110313 @ rn6
Intron Retention
Gene
ENSRNOG00000000480 | Phf1
Description
PHD finger protein 1 [Source:RGD Symbol;Acc:1303205]
Coordinates
chr20:5529640-5529919:+
Coord C1 exon
chr20:5529640-5529708
Coord A exon
chr20:5529709-5529795
Coord C2 exon
chr20:5529796-5529919
Length
87 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
ACAATCTCATGCTCCTCCAGGGT
3' ss Score
9.12
Exon sequences
Seq C1 exon
ATTCTATGAATTTGAATGCTGTGTGTGCCGGGGCGGCCCTGAGAAAGTACGGAGGTTACAGCTTCGCTG
Seq A exon
GTGAGAAGGATGGTGCTCTCCGCCATTTTACTCTATGACTCCTGACTCCATAATGCTGCTGCTGTTGACAATCTCATGCTCCTCCAG
Seq C2 exon
GGTGGATGTGGCCCATCTTGTTCTCTACCATCTCAGCGTTTGCTGTAAGAAGAAATATTTCGATTTTGACCGAGAGATCCTCCCCTTCACCTCTGAGAATTGGGACAGTCTGCTCCTGGGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000480:ENSRNOT00000059548:8
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=PD(25.5=58.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTGAATGCTGTGTGTGCCG
R:
CCAGGAGCAGACTGTCCCAAT
Band lengths:
179-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]