GgaINT1024133 @ galGal4
Intron Retention
Gene
ENSGALG00000005315 | RPUSD1
Description
RNA pseudouridylate synthase domain containing 1 [Source:HGNC Symbol;Acc:HGNC:14173]
Coordinates
chr14:5982462-5982945:+
Coord C1 exon
chr14:5982462-5982743
Coord A exon
chr14:5982744-5982821
Coord C2 exon
chr14:5982822-5982945
Length
78 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CGCACGTCCCTCTGCCCCAGGTT
3' ss Score
8.9
Exon sequences
Seq C1 exon
TGCGCGGGGCCGCAGGAGCGAGCGATGCGGGGCCGCGATGCGCGGTTTTCCCCGGCCCGCCCGGCCCCAGCCCCGCCGCTGTCGCCGCAGGGCGCTCGCCATGGAGCCGGGCACCATCGACAACCTCTGCATCCTGTACCAGAGCCCCGACTTCATCGTGGTCAACAAGCACTGGGACATCCGCATCGACAGCAAGATGTGGTACGAGACGCTGACCCTGCAGAGCCAGCTGAAGCACCGCTTCCCCGAGCTGGCCGACCCCGACACGTACTACGGTTTCAG
Seq A exon
GTGAGCCCCGGGCCGCGGGCGGGGCCGCGCATCGGTGGCCGAATGGCCGCGGTGCTCCCGCACGTCCCTCTGCCCCAG
Seq C2 exon
GTTCTGCCATCAGCTCGACTTCTCCACCAGCGGGGCCCTCTGCGTCGCGCTCAACAAAGCGGCGGCGGGCAGCGCCTACAAGTGCTTCAAGGACCGCCTGGTGACCAAAGCCTACCTGGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005315:ENSGALT00000008518:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0084917=PseudoU_synth_2=PU(26.5=72.1)
A:
NA
C2:
PF0084917=PseudoU_synth_2=FE(24.7=100)
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:
AGATGTGGTACGAGACGCTGA
R:
CTTGAAGCACTTGTAGGCGCT
Band lengths:
179-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]