GgaINT0126425 @ galGal3
Intron Retention
Gene
ENSGALG00000004565 | PHYHD1
Description
NA
Coordinates
chr17:5953559-5954799:+
Coord C1 exon
chr17:5953559-5953685
Coord A exon
chr17:5953686-5954134
Coord C2 exon
chr17:5954135-5954799
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
GCTCCAGCCAACTCCTGAACTGCCTTTTCCACCGCTCTACACGTGATGTTCACAACTGGCTTCTGGAGTCAGCTAGCTCGTCGGTGTTCCCATGATTGCTTGTCTGTGTTCTCTTTAAATGCAGCTCACTAGATCAATGCTCCAGATATAATTATCCCCTGTGAGCAAGCTCCCTTCATGCAGCCAAATCTGCCTGCCTAAGGTAGAAGCTTCTGCTGCAGGATGAGCCCTGCTCTGTGGATAGTAGCCCGCTCCTTTTGGTGAGGAAATTTCTTCTGTCTCCTGAATAGGCCATTAAGGGGTGTTCCACTTTGACCATGACGCTGGTTGAGAAATATTTCTTGTTGCTGAACTGTAGTATTTAAAGTCAGGAGCTCATTTAGTGCTTGGCTCTGTTAATTGGCAGTGCAGGTGAATGTGTGGTGTGAAGATGGCTGACTTTTAGCCTTGGGTCTCTGTCCTATTGCTTGAATAGTAGTAGAAACAATGCTAGTGTGGGCAAAATGAATCAGGAAGTATACTGTTTTAATTAATGACTCTTCTGGGTATTTCTTGCAAATCGAATGCTTGATCTCTAGGCTTGATTAGAAATGTTGTTAAAGATGTTGGAAGTATGAAAATAACAAAACCCCTCATGATACTTAAATAAAAAAAATCATAAACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004565:ENSGALT00000007266:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
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
Rat
(rn6)
No conservation detected
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]