BtaINT0110677 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001634 | PHF1
Description
PHD finger protein 1 [Source:HGNC Symbol;Acc:HGNC:8919]
Coordinates
chr23:7531132-7531538:+
Coord C1 exon
chr23:7531132-7531280
Coord A exon
chr23:7531281-7531442
Coord C2 exon
chr23:7531443-7531538
Length
162 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGT
5' ss Score
6.05
3' ss Seq
CTGGTCCCGTTTCCCTTCAGGTG
3' ss Score
12.22
Exon sequences
Seq C1 exon
AGGGGGGGTGCGCTGAAGAAGGGCCCCTATGCCCGGGCCATGCTGGGCATGAAGCTCTCCCTGCCGTATGGACTGAAGGGGTTGGACTGGGACGCTGGGCATCTGAGCAACCGGCAGCAGAGCTACTGTTACTGTGGTGGCCCTGGGGA
Seq A exon
GTGAGTAGTGAGGGGCGGGGGTTAGGGAACAAGTGATGGGGGTGGGAACAAAGGAGAATTGGCAGGGTGGCGGGAGTGCTGAAGCGGCGGGAGAGTGGTGAGCAGGGTTTGGGGCAGTTAAGGAGGGCGTGTCTGGGGGTCGCTGGTCCCGTTTCCCTTCAG
Seq C2 exon
GTGGAACCTGAAGATGCTGCAGTGCCGGAGCTGCCTGCAGTGGTTCCATGAGGCCTGCACCCAGTGTCTGAGCAAGCCCCTCCTTTACGGGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001634:ENSBTAT00000002140:6
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=PU(14.5=16.0)
A:
NA
C2:
PF0062824=PHD=FE(58.2=100)
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:
GGGGGTGCGCTGAAGAAG
R:
GTAAAGGAGGGGCTTGCTCAG
Band lengths:
234-396
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]