DreINT0129219 @ danRer10
Intron Retention
Gene
ENSDARG00000060192 | rpusd1
Description
RNA pseudouridylate synthase domain containing 1 [Source:ZFIN;Acc:ZDB-GENE-060929-444]
Coordinates
chr3:35414987-35415297:+
Coord C1 exon
chr3:35414987-35415110
Coord A exon
chr3:35415111-35415194
Coord C2 exon
chr3:35415195-35415297
Length
84 bp
Sequences
Splice sites
5' ss Seq
CTGGTATTG
5' ss Score
3.14
3' ss Seq
TATATATATGTCCTCCTCAGGTG
3' ss Score
8.87
Exon sequences
Seq C1 exon
GTTTTGCCATCAGTTGGATTTCTCCACCAGTGGTGCTTTGTGTGTTGCTCTGAATAAGGCGGCAGCAGGTCAAGCGTATCGCTGTTTTAAAGACAGACGGGTTACCAAAGCTTATCTAGCACTG
Seq A exon
GTATTGTGGCATTCAGACATTCAGTCAATACATATGTTTTTTTTTTTATTATAATAACCCAGCCTATATATATGTCCTCCTCAG
Seq C2 exon
GTGCGTGGTACTGTGACTGAGGAGAATCTGAGCCTGGATTTCGCAATTGGCAAGAACACCACGGAGGGCAAAACCCATATGATGTGCACTGAAGGAACGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060192:ENSDART00000146529:3
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=0.171
Domain overlap (PFAM):
C1:
PF0084917=PseudoU_synth_2=FE(24.7=100)
A:
NA
C2:
PF0084917=PseudoU_synth_2=FE(20.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGCTCTGAATAAGGCGGCAG
R:
CCGTTCCTTCAGTGCACATCA
Band lengths:
180-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]