RnoINT0130049 @ rn6
Intron Retention
Gene
ENSRNOG00000000464 | Rxrb
Description
retinoid X receptor beta [Source:RGD Symbol;Acc:3611]
Coordinates
chr20:3824014-3824978:+
Coord C1 exon
chr20:3824014-3824231
Coord A exon
chr20:3824232-3824821
Coord C2 exon
chr20:3824822-3824978
Length
590 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCCTATCTCCCCCATCCCAGATT
3' ss Score
7.97
Exon sequences
Seq C1 exon
ATTCCCGAAGCCCAGACAGCTCCTCCCCAAATCCCCTTTCCCAGGGGATCCCTCCCTCTTCTCCTCCCGGTCCACCTCACACCCCTTCAGCACCTCCACCTCCAATGCCACCCCCTCCACTGGGCTCCCCCTTCCCAGTCATCAGTTCTTCCATGGGGTCTCCTGGCTTGCCCCCTCCGGCTCCCCCAGGATTCTCCGGGCCTGTCAGCAGCCCTCAG
Seq A exon
GTGAGAAGTTGTGACACTTTCAATTCCTTGTTCTCAGCTTCTTACCCCCACCCCCACGCCCCATCTTTGGGTGAACTTCCCCATAACCCGTTGACTGTTCTGGTTCTCTAATCTAAGTAGGCCCATGGTCTCAGACTCCTTGCTCTCTCTGAAGGGAGTGGTCTTTTGGTGCATGATTCTCAGCTCTGTTTTGCAAACAAACAAAAACACTTCAGCCCAAAGGGAATATTTTTGTTGTCCTGTTCAGCTCACAGTGGCCTTCTACCCTCGTCCGTTCAATATGGCCTTCTAAGACGTGCCCTTCAGGGCCACTGTGTAGTGCAATTACAGAAGGTTAGATATCGTTCAGTCATGCCGCAGGAAACCCCTTTACGACAGGCTACAATGTCACCAGTACCCTCTGGGCTTGCTCACAAGTAGGAACTGGTTTTCCTGGGTTGGGGATTTAGCTCAGTGGTAGAGCACTTGCCTAGCAAGCGCAAGGTCCTGGGTTCAGTCCTCAGCTCCGGGGGTGGGGGCTGGTTTCCCTGACATATGAGAGTTGCTTTCCAAATGAGTCTCCTGTGACTTCCCTATCTCCCCCATCCCAG
Seq C2 exon
ATTAACTCCACAGTGTCGCTCCCTGGGGGTGGGTCTGGCCCCCCTGAAGATGTGAAGCCACCAGTCTTAGGGGTCCGGGGCCTGCACTGTCCACCCCCTCCAGGTGGCCCTGGGGCTGGCAAACGACTTTGTGCAATCTGCGGGGACCGAAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000464:ENSRNOT00000041613:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.763
Domain overlap (PFAM):
C1:
PF118253=Nuc_recep-AF1=PU(62.9=90.4)
A:
NA
C2:
PF118253=Nuc_recep-AF1=PD(35.2=69.8),PF0010513=zf-C4=PU(15.7=20.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGACAGCTCCTCCCCAAATC
R:
TTGCACAAAGTCGTTTGCCAG
Band lengths:
342-932
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]