RnoINT0110307 @ rn6
Intron Retention
Gene
ENSRNOG00000000480 | Phf1
Description
PHD finger protein 1 [Source:RGD Symbol;Acc:1303205]
Coordinates
chr20:5528051-5528389:+
Coord C1 exon
chr20:5528051-5528225
Coord A exon
chr20:5528226-5528307
Coord C2 exon
chr20:5528308-5528389
Length
82 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GTCTTGGTCATCCACTCCAGGTG
3' ss Score
8.34
Exon sequences
Seq C1 exon
CCCACCCCAGGATGCAATGGCGCAGCTCCCCCGGCTGAGCCGTTTGGGTGCTCCCTCTCTTTGGGACCCAGCCTCCCCTGCTCCCACCTCAGGCCCCAGACCTCGGCTTTGGGAAGGTCAAGATGTGCTGGCAAGATGGACTGATGGGCTCCTGTACTTGGGCACCATCAAAAAG
Seq A exon
GTGAGGCCCACCTCTGATCCCCTGCCTTCCCAGGCCGGTCTGATTCCTGCCCCCACTTTACGGTCTTGGTCATCCACTCCAG
Seq C2 exon
GTGGACAGTGCGCGGGAGGTGTGTCTGGTCCAGTTTGAGGATGATTCCCAGTTTCTAGTTCTATGGAAGGACATCAGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000480:ENSRNOT00000059548:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.226 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF150571=DUF4537=PU(33.3=35.8)
A:
NA
C2:
PF150571=DUF4537=FE(47.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCTTTGGGACCCAGCCTC
R:
GGGAATCATCCTCAAACTGGACC
Band lengths:
170-252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]