BtaINT0110673 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001634 | PHF1
Description
PHD finger protein 1 [Source:HGNC Symbol;Acc:HGNC:8919]
Coordinates
chr23:7529628-7529967:+
Coord C1 exon
chr23:7529628-7529802
Coord A exon
chr23:7529803-7529885
Coord C2 exon
chr23:7529886-7529967
Length
83 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TCTGTGCTCACCCATTCCAGGTG
3' ss Score
10.33
Exon sequences
Seq C1 exon
GCCCCCCCAGGATGCAATGGCACAGCCCCCCCGGCTGAGCCGCTCTGGTGCCCCCCCACTTTGGGACCCAGCTTCCCCTGCTCCCACCTCAGGCCCCCGGCCTCGACTTTGGGAGGGTCAAGATGTGCTGGCCAGATGGACAGATGGGCTGCTATACTTGGGGACCATCAAAAAG
Seq A exon
GTAAGACCTCTGACCTGTCACATTTTCTCATTCCCCTTATCTAGTCTGATTTCTGTTCCATCTTCTGTGCTCACCCATTCCAG
Seq C2 exon
GTGGACAGTGCTCGGGAGGTGTGTCTGGTTCAGTTTGAGGATGATTCCCAGTTTCTGGTTCTATGGAAAGACATTAGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001634:ENSBTAT00000002140:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.566 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF150571=DUF4537=PU(33.9=35.8)
A:
NA
C2:
PF150571=DUF4537=FE(48.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACTTTGGGACCCAGCTTCC
R:
GGGAATCATCCTCAAACTGAACCA
Band lengths:
168-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]