GgaINT0013245 @ galGal3
Intron Retention
Gene
ENSGALG00000005315 | RPUSD1
Description
NA
Coordinates
chr14:6016930-6017220:+
Coord C1 exon
chr14:6016930-6017003
Coord A exon
chr14:6017004-6017096
Coord C2 exon
chr14:6017097-6017220
Length
93 bp
Sequences
Splice sites
5' ss Seq
CACGTAATA
5' ss Score
1.72
3' ss Seq
ATTAGGCCCTTATGCCCCAGGTT
3' ss Score
5.73
Exon sequences
Seq C1 exon
CAAGATGCATACGAGACGCTTACCCTGCAGAGCCAGTTGAAGCACCGCTTCCCCGATCTGGCTGACCCCGACAC
Seq A exon
GTAATACGGTTTCAGATGAGTTCAGGAGATAGTTGAATTTGCGCATCGCTGGCCGAATGGCCGTGCACCGCCAATTAGGCCCTTATGCCCCAG
Seq C2 exon
GTTCCAGCATCTTCTTGGCTTCTCCACCAGCGGGGCCCTCTGCTTCGCGCTCAACAAAGCGGCGGCGGGCAGCGCCTACAAGTGCTTCAAGGACCGCCTGGTGACCAAAGCCTACCTGGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005315:ENSGALT00000008518:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0084917=PseudoU_synth_2=FE(14.5=100)
A:
NA
C2:
PF0084917=PseudoU_synth_2=FE(24.8=100)
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:
CTTACCCTGCAGAGCCAGTTG
R:
CAGGTAGGCTTTGGTCACCAG
Band lengths:
174-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]