RnoINT0159666 @ rn6
Intron Retention
Gene
ENSRNOG00000008616 | Ubr3
Description
ubiquitin protein ligase E3 component n-recognin 3 [Source:RGD Symbol;Acc:1565257]
Coordinates
chr3:56173697-56175496:+
Coord C1 exon
chr3:56173697-56173827
Coord A exon
chr3:56173828-56175267
Coord C2 exon
chr3:56175268-56175496
Length
1440 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCT
5' ss Score
8.49
3' ss Seq
GCTATTTAAAAATTTTACAGGTT
3' ss Score
6.44
Exon sequences
Seq C1 exon
ATCAATCCATAATGGATGTTTTGAAACATAAAAGTTTTTTAGAAGAACTATTGTTTTGGACAATAAAGTATGAATTCCCCCAGAAGATGGTAACTTTCTTACTCAATATGCTTCCAGATCAAGAGTATAAG
Seq A exon
GTACCTGTTACTTCCTTCCTCTTGGAACTTTGCTTTCATTATTTGTTTATTGTTCAGTCTTTTTCTTTTGTTGCATTTCTTAGCTGAGGCTCATTATAAGATAAATACAAGGATATAATATGAAAGGGTGTTTGTTACTTTCTTGTAGAGAGTCTGCTCAGAATACACAGAATCTCAGCTTTCCTTTGACTTAGCATTGCTCAGCAGAATTCCACAGTGTTGCTATTTCAAATTTTAATTTTAAAATATTATATACACTCTTGTTTAAGGATATAAAATTTTACATGTTCACAGTTACACATCAATTTTATCTTTGTTCTGTGAGGCCTACAACAATAAAAACTGAAGTCCTAGCTAGAAATCCACTAGAGTAACAGTATTAAACAAGTGGAACTCTATGAGAAGGGAGTGGTGGGAGATAAACAGTAATAAAGTGATTGCAGAAGCAAGTAATTTGTAACCTAAGTGTTGAGTCCTCTAAAGGACAGTTACAAGGTGCTGTTATAACATGTAATGGGGTGATTGAGCTTACATTATGGAGTTAGTTAGCATGGTTATGTTGTTATGGGAGAATAGTTACTAATCAAATACAGGTGCAGGGAGGTGAGGTTTCTAGTCCCAAAGGGCATGGATCCACCTCTGAGCACCATATGGTTATGGCAAAATGTATCAACAGAATAAGACACACACTGGGAGAGAACTCTGAAGTCACATTAATTTGGGTCTTTTAATACTCTAACATGTGTAACAGGAAGATAACCTGTGACAGACAGGAAATAACTCCAGCTATAATTGATACTGCAGGCGTTTGGTCAGGTTGCTGGTCAGCTCTCAGAGCAGGTGGGGAGATTATTTCTTGTGGGGATAACCATACCGCCTTGTTTAGTAATGTCACTCTGCTGGTTTCTAGCCAGGACTTTAGGTTTTATATTTGTAGGTCTCATGGAATGAAGACACTTAAAAAGCAAAACAAAACAAACAAACAAAACCAACAGGATTTCTCTGTGTATCCATGGCTGTCCTGGAACTCACTGTGTAGTAGTGTCTTGAACTCAGAAATCTGTCTTTGTCTCCAGAATGCTGACATTAAAGATGTTCACCACCATCACCCTGCTAAGGATACAGTTTCAAAAAATAGATGTAACTTTGAACAAGTTAAGTTTTAAATTCTTGAACCACAGTTTACAATCATTTCGAAACTTAAATGTTTATTATTAGCTTTTTAAAACTATTAAAGTATTTTGGTAATGTTTCATAAAAAGGTAAAATATATGACTTAAAATTTCCATTATTTTAATTACATTTTCATTTACCTTGTATAACATCATTTGTTACTAACAGCTTTAAAAGCTGATTATAATAGGTGATATAAAATACTAACAGATTTTAAATTTGCATTTAGGTTGATGTTTTCTTGTTTGCTATTTAAAAATTTTACAG
Seq C2 exon
GTTGCTTTTACAAAAACTTTTGTTCAGCATTATGCATTTATTATGAAAACACTGAAGAAAAGTCACGAGTCAGACACGATGTCCAACAGAATTGTGCATATTAGTGTCCAGTTGTTCAGCAATGAGGAGCTAGCCAGACAGGTGACAGAGGAGTGTCAGCTCCTGGACATCATGGTCACCGTGCTGCTGTACATGATGGAGAGCTGCCTCATCAAAAGTGAGCTGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008616:ENSRNOT00000011380:7
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:
PF0065015=CRAL_TRIO=PU(3.4=9.1)
A:
NA
C2:
PF0065015=CRAL_TRIO=PU(63.1=84.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGACAATAAAGTATGAATTCCCCCA
R:
TGCAGCTCACTTTTGATGAGGC
Band lengths:
302-1742
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]