BtaINT0110675 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001634 | PHF1
Description
PHD finger protein 1 [Source:HGNC Symbol;Acc:HGNC:8919]
Coordinates
chr23:7530066-7531037:+
Coord C1 exon
chr23:7530066-7530161
Coord A exon
chr23:7530162-7530936
Coord C2 exon
chr23:7530937-7531037
Length
775 bp
Sequences
Splice sites
5' ss Seq
ATGGTGGGT
5' ss Score
6.18
3' ss Seq
TCAATATTCTCATTATTTAGCTT
3' ss Score
6.37
Exon sequences
Seq C1 exon
CGGCGCTCCCTGGGGAGGAACTCCTCTGCTGTGTATGTCGCTCTGAGACTGTGGTCCCTGGGAACCGGCTGGTCAGCTGTGAGAAGTGTCGCCATG
Seq A exon
GTGGGTGAGAGGGCAGGACACCTGAATGGCCTAGCTTGCCCTAGGTCTGCCAGGGTGCCTCTGACCCTTCCCTCCAGCACTGGTCCTGATACTGTCTGTCTTGGTCTGAGTCCCCAAGCTACTGCTCTGGCCAGTCTCCACAAGCCTGTAACCTCACTCCCTTCCAGCACAGGGAGAGGCGGCCTTGGGATAGGATGTATGAGCTCTGCGGGCAGAGGGTGTGAATGAGCAAAAGTCTCTCAGTTGTGTCTGACTCTTTGTGACCTCATGAACCGTACAGTCCATGGAATTCTCCAGGCCAGGATACTAGAATGGGTACTCTTTCCCTTTTCCAGGGAATCTTCCCCACCCAGGGATCAAACCCAGGTTCCCCACATTGCAGGCGGAATCTTTACTAGCTGAGCCACAAGGGAAGCCCACGAATACTGGAGTGGGTAGCCTATCCCTTCTCCAGGGGAACTTCCTGACCCAGGAATCGAACCGGGGTCTCCTGCATTGCAGGTGTTCTTTACCAACTGAGCTATCAAGGAAGCCCCAAATGCAGGCAGAGGGTAGTTCCAGTACGGCTTTTTCTAACCATTTGACCTTGGGCAAGTCCCTAAACTTCTAAGAATCACAGCTGCCTCACCTGCTTTTAAAATAAAGGTAATACGCCCACCCAGCAGGACCATGGTCAAGAACAAAATGAGATGGAGTAAGACTTTTGTCCCAATACGTAGCGCACACAGGTATGCAATGCAATAAGTGGTCTACTGTCAATATTCTCATTATTTAG
Seq C2 exon
CTTATCACCAGGACTGCCATGTTCCAAGGGCCCCAGCCCCTGGAGAGGGAGAGGGCGCATCCTGGGTCTGCCGCCAGTGCGTTTTTGCCATCGCCACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001634:ENSBTAT00000002140:4
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(14.3=24.2),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
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAACTCCTCTGCTGTGTATGT
R:
CTTGGTGGCGATGGCAAAAAC
Band lengths:
182-957
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]