BtaINT0110678 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001634 | PHF1
Description
PHD finger protein 1 [Source:HGNC Symbol;Acc:HGNC:8919]
Coordinates
chr23:7531443-7531784:+
Coord C1 exon
chr23:7531443-7531538
Coord A exon
chr23:7531539-7531715
Coord C2 exon
chr23:7531716-7531784
Length
177 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TTCCTCTTGTCTATGTCCAGGTT
3' ss Score
8.51
Exon sequences
Seq C1 exon
GTGGAACCTGAAGATGCTGCAGTGCCGGAGCTGCCTGCAGTGGTTCCATGAGGCCTGCACCCAGTGTCTGAGCAAGCCCCTCCTTTACGGGGACAG
Seq A exon
GTGAGCCTGGGCAGACCCTCCAGGAGCTCTGCCCCCCATCCCAGACCAGGTGTCTTCCTGACCTCTGAAGCCTTGCTTACCGGTTAGCTCCATCCTTGCTCGGAACACCCCTCCCTCCCCCGTGGGCAGGTGTAGTTTCCTGTAAAAGTGTATTCTCTTCCTCTTGTCTATGTCCAG
Seq C2 exon
GTTCTATGAGTTTGAGTGCTGTGTGTGTCGGGGGGGCCCTGAGAAGGTCCGGAGGCTACAGCTTCGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001634:ENSBTAT00000002140:7
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=FE(58.2=100)
A:
NA
C2:
PF0062824=PHD=PD(25.5=58.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGAACCTGAAGATGCTGCA
R:
CGAAGCTGTAGCCTCCGGA
Band lengths:
162-339
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]