RnoINT0130054 @ rn6
Intron Retention
Gene
ENSRNOG00000000464 | Rxrb
Description
retinoid X receptor beta [Source:RGD Symbol;Acc:3611]
Coordinates
chr20:3827347-3827686:+
Coord C1 exon
chr20:3827347-3827479
Coord A exon
chr20:3827480-3827594
Coord C2 exon
chr20:3827595-3827686
Length
115 bp
Sequences
Splice sites
5' ss Seq
TCGGTCAGT
5' ss Score
7.03
3' ss Seq
ACCTGCAGGTCCCTCTCCAGGGT
3' ss Score
5.34
Exon sequences
Seq C1 exon
GCTGGAATGAGCTCCTCATTGCGTCCTTCTCCCATCGGTCCATCGATGTCCGAGATGGCATCCTCCTGGCCACGGGTCTTCATGTGCACAGAAACTCAGCCCATTCTGCAGGCGTGGGAGCCATCTTTGATCG
Seq A exon
GTCAGTGGCCCTTGGCCAGTCTGGCCTGTGACTAGAAGGGGTGGAGCTGTAGGCTGGTCCGTGTCCAAGGCTGGCTGAGCTGTGACCTTTGAGTGACCTGCAGGTCCCTCTCCAG
Seq C2 exon
GGTGCTGACAGAGCTAGTGTCCAAAATGCGTGACATGAGGATGGACAAGACGGAGCTTGGCTGCCTGCGGGCAATCATACTGTTTAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000464:ENSRNOT00000041613:7
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=0.059
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(24.0=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(52.6=87.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGCTCCTCATTGCGTCCTT
R:
CTGGGTTAAACAGTATGATTGCCC
Band lengths:
218-333
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]