DreINT0170982 @ danRer10
Intron Retention
Gene
ENSDARG00000042508 | ubr3
Description
ubiquitin protein ligase E3 component n-recognin 3 [Source:ZFIN;Acc:ZDB-GENE-030131-1473]
Coordinates
chr9:3985843-3987004:-
Coord C1 exon
chr9:3986900-3987004
Coord A exon
chr9:3986038-3986899
Coord C2 exon
chr9:3985843-3986037
Length
862 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
TATTCTTCAATCTGCTGTAGGAG
3' ss Score
7.01
Exon sequences
Seq C1 exon
ATATGGATGGATCATCAGAACATGTCTGAGCATGTGTTGTGTATGGTGCTGTACCTGATAGAGCTTGGACTTGATAATCAGGTCCAGGATGACAAAGTGGAAGAG
Seq A exon
GTAAGGACATTATCCCTAAATTAAAGAGTGTTTTTGACGCGTGCATTGCTATCAGAAATCAAGAGCTTCTTAAAAGGATAGTTCACCCAAAATGGCAAACTGTCATCATTTAGACACTCTTCACATCTGGTATTAAAATACTTTATCGTTGAGCCAATCACAAAAGAATAAGGCTATATATAGGTGTCAATTGGGTATGAAACATTTTGAGCCTGTCTATGTTGAACTGCATTCGCATAAAAAAATAAAATCTAATTGTGTGTATATACAGGAAATATATGCTTGTATCATTTTCATCTCATCATATACATTTGGTTTATATTTTCATACACAATTTAAAATTTTCATGCGCAATTTATGTTTGGCCATTGTGTTTGGCCATCTGATCGCTATGGCGCCCTCCATGCAGCAGCCATGAAAAAGGTCTATAGACCTGAACAGTGCAGGGGCTTGCTTTATATACACAGAAAAGAAAGAAATCCAAAGATGCCTTTTAAAATTGTAAAGAAGTCTGTGTTTTTGAAATGAATGAAGGCAGCAGAAGTGATTGATTTATTTTAATTATATAGCCTAACATCTTTGTTGTTCTAAAACATTTTAAAAGTTGAATATAATGTGTTGAATAGGGGAAAAAAGTTTTTGTTTTTTACGCAGACTTTCAAAAAGGCCATGTTTTAGAGCAGTAATCCCAATAGCGTGAAACCATTATATTATTATTCAAGGTTATCATACTGTAAGAATCTTATAGCAGCCCATGCCTAGACTAGATTTGTGGCCTCTCGAAACCGTGAGCTTCAGATACTCTAAGAATTCCAGACGCTTGTTTTCTCTTGCTGAGTGTTTATTCTTCAATCTGCTGTAG
Seq C2 exon
GAGCCCTGTATCGAGGAGCACTGCCACGACAGCTGGTTCCCGGGCACCAGCCTGCTGTCTAACCTCCATCACGTCATCAACTTTGTGCGGGTTCGAGTGCCGGAGACGGCTCCGGAGGTGGAGAGGAAGCGAGAGAGGGAACGAGAGAGAGAAACTCCACCCAGCACCAGTTCAGAGAGCGCCACCTTTGGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042508:ENSDART00000129091:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.143 A=NA C2=0.454
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGATGGATCATCAGAACATGTCT
R:
CCAAAGGTGGCGCTCTCTGAA
Band lengths:
294-1156
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]