RnoINT0110309 @ rn6
Intron Retention
Gene
ENSRNOG00000000480 | Phf1
Description
PHD finger protein 1 [Source:RGD Symbol;Acc:1303205]
Coordinates
chr20:5528486-5529034:+
Coord C1 exon
chr20:5528486-5528581
Coord A exon
chr20:5528582-5528933
Coord C2 exon
chr20:5528934-5529034
Length
352 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
GGCCTTCTCTCCTCATTCAGCCT
3' ss Score
7.4
Exon sequences
Seq C1 exon
CCGCCCTTCCTGGTGAGGAGCTCCTCTGTTGTGTGTGTCGCTCTGAGACCGTGGTCCCTGGGAACCGGCTGGTCAGCTGTGAGAAGTGTCGCCATG
Seq A exon
GTGAGAGGGCGGGATGTTTAGGGGGTGCAGTTTGCCCTGGGTCTTCTGGGTTACCACTAGAAGGGTTACCCTCCCTCATAGCGTGAGTCACGCACGTCTCCTGCCTGGGCCAGTCCTCACCCTGTCACCTCATCTCAGTACAGGGAGAGGGAGCGTGGATGCAGGTGACAAGGCTGAGGGCCTACCGTAGCTCGCTCACATTTCTTAACCAAGCTTCCTTGGGCAAGGTCCTCAACTGCTAGAAGCCCGTTGACTCAACTTGAGTGTCAGGATGAGACCTGCCAGCGGGACCGGTCTTAAATGCCCTGGTCAGGACTTAAAGGCCACTCTGTGGCCTTCTCTCCTCATTCAG
Seq C2 exon
CCTATCACCAGGACTGTCACGTCCCCAGGGCCCCAGCCCCTGGAGAAGGAGAGGGCAGCTCCTGGGTCTGCCGCCAGTGTGTCTTTGCGATTGCCACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000480:ENSRNOT00000059548:4
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:
PF150571=DUF4537=PD(15.8=27.3),PF0013017=C1_1=PU(68.3=84.8),PF0062824=PHD=PU(44.4=72.7)
A:
NA
C2:
PF0013017=C1_1=PD(29.3=35.3),PF0062824=PHD=PD(53.7=85.3)
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:
CCGCCCTTCCTGGTGAGG
R:
GTGGCAATCGCAAAGACACAC
Band lengths:
193-545
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]