RnoINT0130048 @ rn6
Intron Retention
Gene
ENSRNOG00000000464 | Rxrb
Description
retinoid X receptor beta [Source:RGD Symbol;Acc:3611]
Coordinates
chr20:3823042-3824231:+
Coord C1 exon
chr20:3823042-3823407
Coord A exon
chr20:3823408-3824013
Coord C2 exon
chr20:3824014-3824231
Length
606 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
CTTATGTACCCACTTCTCAGATT
3' ss Score
6.77
Exon sequences
Seq C1 exon
CCGAGCCGAGCGCGGCGCTTGAGTCGCGCTGCCACAGGCCGGAGCCCGCCCTCCTCGGCGGCTTCCTCGCGCTCCCTGAGTCCCCCGCTCTGCCCCCTGCGCGTCCCTGGCGCCTCTCCGGCTCCCCCACCCTCGGCCCCGGCGTCATGTCTTGGGCCACTCGTCCGCCCTTCCTCCCGCCGCGGCATGCCGCGGGGCAGTGTGGGCCGGTGGGGGTGAGAAAAGAGATGCATTGTGGGGTCGCGTCCCGGTGGCGGCGGCGGCGGCCCTGGCTGGATCCCGCGGCGGCGGCGGCCGGAGAGCAGCAAACCCTGGAGCCGGAGCCGGGGGAGGCTGGCCGGGACGGGATGGGCGACAGCGGGCGGG
Seq A exon
GTGAGTGTCCCGTGGGCCCGGGCCGGCGCCCCTCGCGCCCCCTCCCCGCTCTCCCGCCCCCTTGTTTGTAAACACGCGCCCTCTCCATCCCGAGGCCCAGCGCCCTCCCCCGGGGCGGGGCGCGGCGGGGGAGCTTCCGCCCTCCAGGTGCGGCGCCGCGGGGCCAGTGTGTGCGGTCTCGGGCGTGGGAAGGACACCATTCCCCTTGGGCTGGAGGACTCTGGGCTTTGGAAGGCTGAGCTTGCGCTCTGGGACTGGGTATATCTTCCATACTCTTCGCCCCGAATGTTCTAAGTTGGGAACGAGGGGTTCACTGGTGCACCTCCACGTGCTTCTTGACACCCCCCTCCCGAGGTCAGCTTGGGATGACCCAATAGGCTCCGCCTGAACTGCCTCCCTTTTTTTTTTTTTTTTTTTTTGTCAACCGCCTCCTCTCCCAGCTTTTAGGAGTGAAATTGTTTGATGACTTGGTGTTTCTGAACTCTGGGGTTGTGGGCTGTGGTGGATCGGGGAGAATTAAAAGTGTCCATTTGGGTGATCGAGAGACTCAACTTTCTCTTCTTGTCTCTCCTGTCTGTGTGTCTGTCTTATGTACCCACTTCTCAG
Seq C2 exon
ATTCCCGAAGCCCAGACAGCTCCTCCCCAAATCCCCTTTCCCAGGGGATCCCTCCCTCTTCTCCTCCCGGTCCACCTCACACCCCTTCAGCACCTCCACCTCCAATGCCACCCCCTCCACTGGGCTCCCCCTTCCCAGTCATCAGTTCTTCCATGGGGTCTCCTGGCTTGCCCCCTCCGGCTCCCCCAGGATTCTCCGGGCCTGTCAGCAGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000464:ENSRNOT00000041613:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF118253=Nuc_recep-AF1=PU(62.9=90.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAGATGCATTGTGGGGTCG
R:
GACAGGCCCGGAGAATCCT
Band lengths:
350-956
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]