RnoINT0110308 @ rn6
Intron Retention
Gene
ENSRNOG00000000480 | Phf1
Description
PHD finger protein 1 [Source:RGD Symbol;Acc:1303205]
Coordinates
chr20:5528308-5528581:+
Coord C1 exon
chr20:5528308-5528389
Coord A exon
chr20:5528390-5528485
Coord C2 exon
chr20:5528486-5528581
Length
96 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GACACTTTGTTCTCTCACAGCCG
3' ss Score
8.99
Exon sequences
Seq C1 exon
GTGGACAGTGCGCGGGAGGTGTGTCTGGTCCAGTTTGAGGATGATTCCCAGTTTCTAGTTCTATGGAAGGACATCAGCCCAG
Seq A exon
GTGAGACCCTTCAAAGCACAGCTTCCCTCTGCAGCAGCTGGAGCCGATGGGGACGCTGGGTTGAAGTGGGCCTCCTGACACTTTGTTCTCTCACAG
Seq C2 exon
CCGCCCTTCCTGGTGAGGAGCTCCTCTGTTGTGTGTGTCGCTCTGAGACCGTGGTCCCTGGGAACCGGCTGGTCAGCTGTGAGAAGTGTCGCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000480:ENSRNOT00000059548:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF150571=DUF4537=FE(47.4=100)
A:
NA
C2:
PF150571=DUF4537=PD(15.8=27.3),PF0013017=C1_1=PU(68.3=84.8),PF0062824=PHD=PU(44.4=72.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGGTGTGTCTGGTCCAGTT
R:
CGACACTTCTCACAGCTGACC
Band lengths:
159-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]