BtaINT0111164 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038831 | PHYHD1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:HGNC Symbol;Acc:HGNC:23396]
Coordinates
chr11:99456940-99458026:+
Coord C1 exon
chr11:99456940-99457056
Coord A exon
chr11:99457057-99457899
Coord C2 exon
chr11:99457900-99458026
Length
843 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGG
5' ss Score
7.81
3' ss Seq
ACCTGCTGTGGCCCTGCCAGGGG
3' ss Score
6.92
Exon sequences
Seq C1 exon
GTGGAGTGTCAAGAAGGATGGTCCGGACCCCTGCTGGCTCAGTGCCTGGCACCAGCTTCCTCGGGTCGGAGCCAATCCGGGATAACAGCCTCTTTGTGCCCACACCAGTGCTGAGAG
Seq A exon
GTAGGGGGGGTGCAGAGGGCAGGGAGCAGGGCCTGGAGGCCATGCCCAGGGGGTCTGTGCCTGCTCTGACCTGAGGGCCGGGGAGTCACAGCAGGAGGGAACGTCGGGCGGGCGCTTCGAGGACTGAAAGCTGCGTGACCGACACCAGGGTCCCCCAGGCTGGCCTGGAATCCAGATACTGCTCCTTCCAGACTGTCTCTAAGAGCAAATGACTGAAACCCTCTGAGCCTCAGTTTCCCCAAACATCAAGTGGGGAAGCCAGTGAGATGTCATGTGTGAGATGGTGCACAAGTGCTCAGAAACCCTGGCTGTCAGCACACCCTTCCTTTCGATTTTTGTATTAGTATTTATCTGGTTGCATTGGGTGTTAGTTGTGACGAGTGTGCTCAGGAGTTGAGCCATGCAGGCAGCTGCCTCGTGGCACGTGGAAGTCTTAGTTCCCCAGCCAGGGATTGAACTTGCATCCCCTGCATGGGAAGGCGGTTTCTTAACCACGGGACCACCAGGGCAGTCCCACACCCTTTCTTTTAGAAAAGGGAAACTGAGTTCCAACGCTGTGTTCCTGGGTGAGGCCCCAGCTGGCTTCTGCCTGGTTCTGGAAATGCCGCAGAAGGCAATGCCACTGCCGAGGCTTGCGAGGGCATGGGCCACGGTGGAAGGACTTGATCCCGGGGCAACCCACGTCCAACCACACAGCCTCCAACCTGGGGCAGACTCCAGGCCCCTGAGGTTGCCAGGATGAGGGTGGGGACAAAGAGGCCATACCACCGCTTGAGGGAGGGGACTGCCCATCATGTCCCTTCCTGCCCCGAGTGCTCTCCTGACCTGCTGTGGCCCTGCCAG
Seq C2 exon
GGGCCCTCGTCCTGATCCACGGAGAAGTGGTTCACAAGAGTGAGCAGAACCTTTCTGACCGCTCGCGCCAGGCCTACACTTTCCACCTCATGGAGGCTGCTGGCACCATCTGGAGCCCAGATAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038831:ENSBTAT00000055396:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.150 A=NA C2=0.023
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:
GGAGTGTCAAGAAGGATGGTCC
R:
CTCCAGATGGTGCCAGCAG
Band lengths:
230-1073
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development