DreINT0172039 @ danRer10
Intron Retention
Gene
ENSDARG00000036833 | upp2
Description
uridine phosphorylase 2 [Source:ZFIN;Acc:ZDB-GENE-040426-830]
Coordinates
chr9:16169960-16170459:-
Coord C1 exon
chr9:16170345-16170459
Coord A exon
chr9:16170170-16170344
Coord C2 exon
chr9:16169960-16170169
Length
175 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGC
5' ss Score
8.72
3' ss Seq
CCTTTTCTTTGACTACACAGGCT
3' ss Score
7.86
Exon sequences
Seq C1 exon
CATGGCATGGGTGTTCCCTCCATCTCCATCATGCTGCATGAGCTCATTAAATTGCTCTATCATGCTCGCTGTCGTGATGTCATCATCTTTCGCATTGGCACATCAGGTGGAATTG
Seq A exon
GTAAGCACTTCTTGTATCACAGACATGTAAACCAAAAATACATCACTCTAAAAATGTTTAATGATCAATTCTAAGCCATTACATATAAGAGCCTAGTATTGTTTGAAGAAAAAAAAGGTTTACTGCTCTGTAATTCTGGAGAAAGGGGATTTAAGCCTTTTCTTTGACTACACAG
Seq C2 exon
GCTTGGCTGCAGGTACAATAGTGATCACAGATAAAGCTGTGGACTCATTCTTCAGGCCACAGTTTGAGCAGGTGGTTTTGGGAAAGGTAATCACCAGGAGCACAGAGCTTGATGTGGATATAGCCCAAGAACTACTGCAGTATTCATCTGAGCTTACAGATATGCCCACTGTAATTGCAAACACAATGTGCACGCATGATTTCTACGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036833:ENSDART00000053473:4
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:
PF0104815=PNP_UDP_1=FE(15.1=100)
A:
NA
C2:
PF0104815=PNP_UDP_1=FE(27.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCATGCTCGCTGTCGTGATG
R:
ATGCGTGCACATTGTGTTTGC
Band lengths:
254-429
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]