DreINT0129218 @ danRer10
Intron Retention
Gene
ENSDARG00000060192 | rpusd1
Description
RNA pseudouridylate synthase domain containing 1 [Source:ZFIN;Acc:ZDB-GENE-060929-444]
Coordinates
chr3:35412940-35415110:+
Coord C1 exon
chr3:35412940-35413133
Coord A exon
chr3:35413134-35414986
Coord C2 exon
chr3:35414987-35415110
Length
1853 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATT
5' ss Score
8.55
3' ss Seq
TGTGTTCTTATATTCTGCAGGTT
3' ss Score
10.26
Exon sequences
Seq C1 exon
GAGAAGACGAGCATGGAGCCTGCGAGCCTGGAAAACCTGTGTGTTTTGTATCAAAGTACAAACTATATAGTTGTCAACAAACACTGGGACATTCGAATTGACAGTAAAATGTGGTATGAGAAGCAGACTGTCCAGAGTCAGCTAAAGCATCGCTTTCCAGAGCTTGCAGATCCTGGCACTTACTACGGCTTCAG
Seq A exon
GTAATTTAGTTGTTTTTTAAATAAAATATCCAGCCTCTTCTCATAGTTCATGTTTCACATCACAGGTTTACTACACTTTTGAAAGTAGTTGAATGTCAAACATGGATTCAAGGCCTGGAAATTACTTTAAAATAGGTAATTGAAAGTGCTTGAATTAAATCTGAAAGGGGGTTTGTAGAATTAGACATTCGGTTTCAAACCAATTAAATTCTTTGCTCCTGTTATAGTTTGAGCCAAAAATATGTCAGATAGACATAAATATATGCCCTTTTTGTAGCACAAGACTTAATGTCTCAATTAAAATAAAATAAATAATTAATAATACGAATGAATTGAACAATTCAACCAGTGTAATATTTAAGATTTAAAATCGTACTTTTCAATTTCATACAAGAAGTAAAGCCCCAGTCAGATACCACAATTTCAGCACAATTTCCTGACTCATTAGGGTGTCATTGGGAGTCTTAAATGACAAATTAGTGTTGTGACACAAGATTCAATAGTTTTCCTTGTGTAATGTGGCATAATTCAATTTCTCAGTTATATTCACGGTGATGCTGTCAGTCTGCAGGTCAGGTAATCAAAAAAAGGCTGCATATTTAGCCTACTTATGGGTCGGTCACGGGGTGGATAAGATTAATCATTGGTTATGCAAACTTTAACTACTTTCTCTAAAATATTAAATTGTTTTAAGCAATTTTAACTGACAGACTGACACAAATATACAGACATTTCCATTCTCACAACAAGTTTCTAAGTTCTATCAGCCTTCCGACTGAGTTCGTTTTTTCAAGGTAATCTGGAAGCGCGTTCATTATTCAATATACTTGATTAAATGATTTAAATTGAAAGCCACTGGCAATGGATGATTTTGTCCTTAAATATAGGTTTCTCTGAAGTGGTGACTTTAATTCTATTTAGGCTAGTTGTTTATTTATTTTTTTAACCAGTTTGTGTTCTGAAGCATATAGTGGACTGATTTGAAACACTTCACCTCAGATGTTATTCGATATTGTTGTTTATCTAGTTGATGAAGATACAAATTATACCAAATGAAATGCAAGAAAAATATACATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAATTTATTTAATTATTTAATTAATACTCCACTGTAATTGTTGTATCATAAACCTCTGTCATATATTTGCTATTTTTTCAATATGTCATTATTTTAAACATAATGTTTTTATTTCCTTGTTGCTGATGTGCTTTAATTTTCTCCATCTCACTCATAGCAAGTTTAGGCTAGGAGTGTTTAATAAGCAAGCCATGGCTAAAAAATGTAGATTTCAAAGCAAATATTTACTATTAAAAAGGAAATAAATGTTTGATCCTATCCATGTCATAACGAATGCCCTTAAATAATGTAGCCTAGTTGTCAGCAAGCATCAGTGTTTATTGAGATTGACACGAGATAGGAAATACTGTTATAGCAACACTTGTGACTGCTTTAGGAAATAACTCTCGTCGTAGATGTCACAGGATGACTGATCGTAAAGGAATGTGTAGTCTGGCTCATTTGTTACCCACTATCTTTAAACATGACATATTTTTTGGGGGAATTGACGCGTTCTAAACATCATCATTACATTGACATTTTAATATAAATATTAAGTGTAAGTGAAATGTAAAGTACAGTAAGGACTTTCATGATGCTACGTATGCTGGGATAATTATGAAAGGTGCTTGATTTTAAAATAAAGAGTGCTTTTAGTCCTTTTCCTTGAATCTGCTGTTTATGAAAGAGAGGGAACCCTGTGATCAGCAGTTTGATCATGTGTGTTCTTATATTCTGCAG
Seq C2 exon
GTTTTGCCATCAGTTGGATTTCTCCACCAGTGGTGCTTTGTGTGTTGCTCTGAATAAGGCGGCAGCAGGTCAAGCGTATCGCTGTTTTAAAGACAGACGGGTTACCAAAGCTTATCTAGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060192:ENSDART00000146529:2
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
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAAGACGAGCATGGAGC
R:
GATAAGCTTTGGTAACCCGTCTGT
Band lengths:
310-2163
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]