GgaINT1021467 @ galGal4
Intron Retention
Gene
ENSGALG00000004565 | PHYHD1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:HGNC Symbol;Acc:HGNC:23396]
Coordinates
chr17:5398692-5399935:+
Coord C1 exon
chr17:5398692-5398818
Coord A exon
chr17:5398819-5399267
Coord C2 exon
chr17:5399268-5399935
Length
449 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGG
5' ss Score
6.35
3' ss Seq
TGCTCTTCCTTCCCACTTAGGCT
3' ss Score
9.75
Exon sequences
Seq C1 exon
GTGGGCTCATTGTCATCCACGGAGAGGTCGTCCATAAGAGCGCAATGAACAGCTCGGCGTTCTCTCGCCACGTGTACACCTTCCACGTGATGGAGGCCGAAGGCACCAACTGGAGCAAGGAGAACTG
Seq A exon
GTAGGGTTGCTGTGATTCTTAGACAGATTGTTGTTTAATGAAAGCTTTTCAGTTGTACCTTGGTGCGTTTACAGGCTTCTTGAAGTCGTGCTCAATAAGCATATGGGAGGTAAGGAAAAATGCCATGCTTGGCAATCCTTGCTGTGCTTCCACTTAGCGAAACATGCAACCACGTGCCCTAGGGACATCTCCCAGTTTCCAGGATTTCTATTTAACTTAAAATAAAACAGCTGAGTGCCTGAAAGACAGAACCAATGACTGCAGGGATAACTGGCATTCAGACTGAGGGCTTCCAGAATGCTGGCTTCTATTCTCACTCCATCAGGTCTTGCCGTGGGAGCTGCTGGTTGAGGCGCCCCTTTGGGTGCAGCAGTGCTGATTGCTGATTTAATGCCCCAGAACTGGAGTAGTGACTGCAGTTTTCTTTTCTGCTCTTCCTTCCCACTTAG
Seq C2 exon
GCTCCAGCCAACTCCTGAACTGCCTTTTCCACCGCTCTACACGTGATGTTCACAACTGGCTTCTGGAGTCAGCTAGCTCGTCGGTGTTCCCATGATTGCTTGTCTGTGTTCTCTTTAAATGCAGCTCACTAGATCAATGCTCCAGATATAATTATCCCCTGTGAGCAAGCTCCCTTCATGCAGCCAAATCTGCCTGCCTAAGGTAGAAGCTTCTGCTGCAGGATGAGCCCTGCTCTGTGGATAGTAGCCCGCTCCTTTTGGTGAGGAAATTTCTTCTGTCTCCTGAATAGGCCATTAAGGGGTGTTCCACTTTGACCATGACGCTGGTTGAGAAATATTTCTTGTTGCTGAACTGTAGTATTTAAAGTCAGGAGCTCATTTAGTGCTTGGCTCTGTTAATTGGCAGTGCAGGTGAATGTGTGGTGTGAAGATGGCTGACTTTTAGCCTTGGGTCTCTGTCCTATTGCTTGAATAGTAGTAGAAACAATGCTAGTGTGGGCAAAATGAATCAGGAAGTATACTGTTTTAATTAATGACTCTTCTGGGTATTTCTTGCAAATCGAATGCTTGATCTCTAGGCTTGATTAGAAATGTTGTTAAAGATGTTGGAAGTATGAAAATAACAAAACCCCTCATGATACTTAAATAAAAAAAATCATAAACCTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004565:ENSGALT00000007266:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.047 A=NA C2=0.067
Domain overlap (PFAM):
C1:
PF057218=PhyH=PD(9.7=55.8)
A:
NA
C2:
NO
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:
GGTCGTCCATAAGAGCGCAAT
R:
GAGCGGGCTACTATCCACAGA
Band lengths:
356-805
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]