GgaINT0132389 @ galGal3
Intron Retention
Gene
ENSGALG00000004029 | PHF12
Description
NA
Coordinates
chr19:5873177-5873681:-
Coord C1 exon
chr19:5873629-5873681
Coord A exon
chr19:5873366-5873628
Coord C2 exon
chr19:5873177-5873365
Length
263 bp
Sequences
Splice sites
5' ss Seq
CTGATGGAG
5' ss Score
-11.57
3' ss Seq
CCTCTGTGTGTGTGTGCGTGTCC
3' ss Score
-9.38
Exon sequences
Seq C1 exon
GAGAAGATGGAGACGAAGACGATCGTCTACGACCTGGACACCTCCGGGGGCTG
Seq A exon
ATGGAGTGAAGGGCGGCGGGGCGGTGGGCTTCAAAATGGCGAGGGGACCCCCCCCTTTCACCTCCCCCCCCCCCCCCCCCCGGCCCCGAGCCCCGTGGCCATAGAAGGAAGTGCGGCCGCTCGCCCAATCCCCGGTGGGGGCCCTCCCGGGCACGGACGGGGCGGGCTCGGCCTTATCCCGGCCCCACTGAGCCGTGCGCTGTGGGGGGCGGTGGGGGTCAGAGTGCGGGCGGCCCTCAGAGCCCTCTGTGTGTGTGTGCGTG
Seq C2 exon
TCCGCAGCAAATCCAGGCCCTGCTGGCTCCCCCTAAGAGCGAAGATGGGGAGAAGAGGAGCAGGAGGCCTGAGAAGGAGCCCAGGAGAAGTGGCAGGGCCACTAACCACGACAGCTGCGATAGCTGCAAGGAAGGAGGGGACCTGCTGTGCTGCGATCACTGCCCCGCCGCTTTCCACCTCCAGTGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004029:ENSGALT00000006417:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.547
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0062824=PHD=PU(52.1=39.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAAGATGGAGACGAAGACGA
R:
CAGCACTGGAGGTGGAAAGC
Band lengths:
242-505
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]