DreINT0172036 @ danRer10
Intron Retention
Gene
ENSDARG00000036833 | upp2
Description
uridine phosphorylase 2 [Source:ZFIN;Acc:ZDB-GENE-040426-830]
Coordinates
chr9:16171160-16171735:-
Coord C1 exon
chr9:16171492-16171735
Coord A exon
chr9:16171275-16171491
Coord C2 exon
chr9:16171160-16171274
Length
217 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGA
5' ss Score
10.53
3' ss Seq
ACTTGTTTAATGTGTCATAGACA
3' ss Score
6.36
Exon sequences
Seq C1 exon
AAATAAATATAAATATATTTATATGTGTGTGTTTGTGTGTGTGTAGAAAGTCTGTAGAAGTCAGAGGTCTGTAAAGAGAGAAAATCAGTAGGATATATCAAAAGGATTGTTTTTTTTCTAAAAATACTTTTCTAATTCTGCATATATTTTTATTGATATCTCTGTAAACAATTTTTTTTTTGAGAAGAATCATGGCACTTATTTTAATAAACAACACTGGAAATAAGCACAACAATTATATTCG
Seq A exon
GTAAGAAAAACTTGATCTCGACTTTTATTTCTAAAACTCACCATTTACTGAAATATTTTAAAAAAATGTTTTGTATAAAATAGCTCTTTTTTGGTAAAATACAGTTCCTATGTGTTCTAACCTTCCATAAGCATTAACAGTTTATGTTAACATTCAATGTATAACAGATTTGTTTTTCACTGTCTATTATAACAGTAACTTGTTTAATGTGTCATAG
Seq C2 exon
ACAGGCGAAGTATGTGAATAATCCTCATCTGGATGGCATGGAAGAGGACATCTTGTACCATTTCAGCCTGAGCACCAAGACCCATGACCTGCCCCAGATGTTTGGCGATGTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036833:ENSDART00000053473:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.056 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0104815=PNP_UDP_1=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGTGTGTTTGTGTGTGTGT
R:
TTGGTGCTCAGGCTGAAATGG
Band lengths:
299-516
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]