GgaINT1021475 @ galGal4
Intron Retention
Gene
ENSGALG00000004565 | PHYHD1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:HGNC Symbol;Acc:HGNC:23396]
Coordinates
chr17:5398460-5398818:+
Coord C1 exon
chr17:5398460-5398576
Coord A exon
chr17:5398577-5398691
Coord C2 exon
chr17:5398692-5398818
Length
115 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAA
5' ss Score
6.33
3' ss Seq
TGGGTGTTTCTTGCAACCAGGTG
3' ss Score
8.46
Exon sequences
Seq C1 exon
GTGGGATCACCCGCAGAATGGTGCGTGCAGCCCAGGGTGCCTCGACGTGCGTGGAGTTTGTAGGGTCAGAGCCAGCCTACGATGACAGCAAGTTCATACCTGTGCCCATAAGCAAAG
Seq A exon
GTAGAAGCACCTCAGGGAAGGGAAATACAATTTTATTCCAACAGTTGTACTTTCCTTATGTTACATTTAGCACTCACAATTGGAATTAAGCAGTCTGGGTGTTTCTTGCAACCAG
Seq C2 exon
GTGGGCTCATTGTCATCCACGGAGAGGTCGTCCATAAGAGCGCAATGAACAGCTCGGCGTTCTCTCGCCACGTGTACACCTTCCACGTGATGGAGGCCGAAGGCACCAACTGGAGCAAGGAGAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004565:ENSGALT00000007266:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.047
Domain overlap (PFAM):
C1:
PF057218=PhyH=FE(15.7=100)
A:
NA
C2:
PF057218=PhyH=PD(9.7=55.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATCACCCGCAGAATGGT
R:
GTTCTCCTTGCTCCAGTTGGT
Band lengths:
239-354
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]