DreINT0129217 @ danRer10
Intron Retention
Gene
ENSDARG00000060192 | rpusd1
Description
RNA pseudouridylate synthase domain containing 1 [Source:ZFIN;Acc:ZDB-GENE-060929-444]
Coordinates
chr3:35412559-35413133:+
Coord C1 exon
chr3:35412559-35412839
Coord A exon
chr3:35412840-35412939
Coord C2 exon
chr3:35412940-35413133
Length
100 bp
Sequences
Splice sites
5' ss Seq
CAGGTTATC
5' ss Score
-0.23
3' ss Seq
TATATGTTGTGTTTGTGCAGGAG
3' ss Score
7.92
Exon sequences
Seq C1 exon
AGCATGGGACCAGTAATATAGCATTAAAGTAAATTTATTGAATCTACGCTGACACGTTGGAAAAAAAACTAACGTTCTTAAACAATTACTGAAGATGAACGTGTGCACGATCTGATGATTCCTCTAAAGGAGAAGGTTTGCTCTGCAGAGGGAACATATAAACAGAAGACTGGACGCGAGTGATCCACAGGCAACATGATTATCAACAACATTTAAGTCAGGATCCTTTTCGATACAAGTACAGCGGTAACACGCCAAGCAGCACGCGATAACCACGCCAG
Seq A exon
GTTATCAATAATTCTATTAGTCAATATAAAATATCATATTTTGTCACAAATGTTGACGATTTAATACAACCAGTATAACCTATATGTTGTGTTTGTGCAG
Seq C2 exon
GAGAAGACGAGCATGGAGCCTGCGAGCCTGGAAAACCTGTGTGTTTTGTATCAAAGTACAAACTATATAGTTGTCAACAAACACTGGGACATTCGAATTGACAGTAAAATGTGGTATGAGAAGCAGACTGTCCAGAGTCAGCTAAAGCATCGCTTTCCAGAGCTTGCAGATCCTGGCACTTACTACGGCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060192:ENSDART00000146529:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0084917=PseudoU_synth_2=PU(26.5=72.1)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGAGTGATCCACAGGCAACAT
R:
ACTCTGGACAGTCTGCTTCTCA
Band lengths:
243-343
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]