RnoINT0130040 @ rn6
Intron Retention
Gene
ENSRNOG00000009446 | Rxra
Description
retinoid X receptor alpha [Source:RGD Symbol;Acc:3610]
Coordinates
chr3:6272561-6276637:+
Coord C1 exon
chr3:6272561-6272826
Coord A exon
chr3:6272827-6276486
Coord C2 exon
chr3:6276487-6276637
Length
3660 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCCCAATGATTCTCTTGCAGCTC
3' ss Score
8.39
Exon sequences
Seq C1 exon
ACTTCTCTACCCAGGTGAACTCTTCATCCCTGAGCTCTCCAACGGGTCGAGGCTCCATGGCTGCCCCCTCGCTGCACCCTTCCCTGGGTCCAGGACTCGGCTCTCCTCTGGGCTCCCCTGGGCAGCTGCACTCGCCTATCAGCACCCTGAGTTCTCCCATCAATGGCATGGGCCCACCCTTCTCGGTCATCAGCTCCCCGATGGGCCCGCACTCCATGTCGGTACCCACCACACCCACACTGGGCTTCGGGACTGGCAGCCCCCAG
Seq A exon
GTGAGTGCTGAGCTGAACTTTGGGGACATGGGACAGAAAGTGGGGCAGAAAGTGTAGACTTTGAAGCAGTAGGTCAGAACTGAGATGTCTTTTTCTTCACGGGAGTGGGCTACAGAGCAAAGGCCTCATGCTGGTAGAGTTAGGGATGAGCCTCGCTCTGGCTCCTATAGCTCTGCCAGTTGAAATTTCCTGTAGCTGGTCTTCAACTCAGCCTGGAGCCTGCCCCCATGGCTGTGGAACTCGGGGGCATCTGCTTCCTCAGGCTTGGGGACATCTTTCAGGGTCCCCTGGGGCTCATAGGTTCCTTGTCCCCGGACGCTGGACTCAGTATCCCTAAGCCTTCAGGGAAAGCACATCCTGGCCCTGGATGCCCGTCCCTGGGTTCCATAGAGGCCCTGGTTGCAGCCGATGTGTGGGCTCTGGCTCTCTGTGGCTCTGCGCATGGTGGCTATCTGCAAGATATGACTTCCTTTCCTGTGGCCCTGGTCCTGCTCTGGGCACTCTAGGGGTCTCACTCAGCCTCTTCCTCCCAAGGCCCTGAATACCTGTTATAGTGCCTCTCCCTGCTTCTATTTACTTGAGGGTCTTGGTGAGTTTCTACCTGGATTTTTTGTCCTTAGTGTACATGAAGCTCTGTATCTGGAGATCCAGCTCCTTGGGGTTCCTCTCTCCCTTTCTGAAACAAGTCAGGGATCCCCTTTTGGCTCTGAGCTTCTTAGGTTGGGTTCGTTCTCTCCTCCCCCAATAGCTTTGCTGTTCCACCTCCCATTGGCATGTCTGGGACCCCTCACTAGAACTAAAGGGCCAACAGCCCCTATGTGTCCCTTAGATTTCCAAAGCCTTTTGCCCTGAGCCACGCTGTCTCCTGTGTTGGAGTATGTGGAGAGGCCGGCCACTCACACCTCACCAGGTAGCCTGTTGAGACTGGTCTGAGCTTCTTAAGCTTCTCCCCCAGACAACCTGGCTGCTTTTTCTAGGTTGATTCCATCTAAGCCTCTTTGCCCTAGTCAGTCTCTCCCTCTCCCTCTCCCTCCCCCTCCCCCTCTCCCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGACAAGCCCCTGCACACATAGAAGAGCTAGGCTCCTGTTTATGAGCAGTCTGTTACACTGTCCCTGGCGGCTCCTCACCTTGCTTCTCAGAAGCAGACAGAAGGCCTGAGGTGCTGCTGTCTGTGACCACCTGTGTGCAGGCATGAAGCAGGCCTGACCACCTCCCCTGCCTTGGCCACGTTATTTTTGTCATACCTTCTCTATACCTTTGCTAGGAAGCCATGAGTGGGGAGGGTAGATGAAGAACTGATCTCCGAAGTTCCCTGGCCTCAGAGTTGGCCCCTCTTGGCTCTCAGCTCCGTGAGGCTCCTCGCCAGGTCTGGATATATCTCTACCAGGCCATGGCCACCCAGTGCCCAAGCCACCCGTGTGTCTCATTTGTTTTGGGGGCTCTACTAGGACAGGGCCCTGGGGGTGTTCCCCACCATGTCCCAAACCTGACTGAATGGCCGTGCTGGGCTCTCTGGGTAATTTACAACTGGGAAGCGTTTCTGACCGCCCAGATGAGGAGCGAGTGAGCAAGGCATGGGGGCCTCTGAGGCTCTTGCACTGTGGGTGCCACAGTGACTTTGAAAGCTTGGCGAGCATGCAGAGGTCAGAGAGAAAGAGAGGAGAGGGAGGGAGGGAAGAGGAGGGAAGAGAGAGAGGGAGGGAGGAAGAGGAGAGGGAGGGAGGATGAAGAGAGAGGGAGGGAGGGAGGGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGAGAGAGGGAGAGAGAGAGGGAGGAGTGAGCGAGCAGGTCTGCTCTGGATACCTCATCCGAGTGGACCTAGGTAAGGGCTGGCCTGGGCTTAGGGGGACAGGATGAGGTAGGAGGGGAAGAGGGGATGCCTGAGAAGTAGGTGGGGGCCCAGGTGCGGTACTGCTAAGGCAGAACTGAAATAAATGCCAAAGATATGAAAGGGGAAATGGGATGGCTCCACCCAGGGAGGCTTCGAGCTTCAGCACAGGGCTGCCCAGTCCTGGGCCTCTTGAAACACGTGTCGGGAGCACAGGAGCCCCAGTAGGATGGGAATGTTGAGGAAGGGGAGAATAGAAACTGTCCTGACCCATCAGCTCAGACCCGGGAAGGGCAAAAACAAGCGTCCCCCAAGCCATGGGATTCCCAATTGCCCACTAGTGGAGCTCCGGGGAGCCTCATGCGTGTCTCAGGGCCAGTAGTGGGGTTCGGTGCTACCACCCAACCTTTGCTCTGCTCTGACAGCAGGGTTTCCCAGAGCCAAGACCTCCAGAAACCTGCAGGGTTAGGCTTCCCACACAGTGACTGGAGTGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGCAGTCTTGCCAGCAAAAGCTGGCTATGTCTCCCTGCTGCCCCAGGATTCCCACATAGGGCCTTCAACCAATGAACACATGGACTGTTCTCTTCTGCCATGAGATGTCCTGCCTGCCACCAAAGCCTTTCATGTCTTGACAACTCCCTCTCACACACTCAGGGTTCTCTATTTGGGCCTTCAGGCTTCCCAGGCAGCCCACCCAAAGCTAGCCAGAGTGAGGCATTCTTGCCTAACCTCGCCAAACCTCACCAAACCTCACCAAACCTCACCGCCTGGCCGGCTGGGGCTGCGAAATCATTCTGGATTCCAGGCCCCCTCCGTTCTTTCGCTGTCCCGTGAGAAAGGGGTGGGGGGATGGGGCAGGAGGAAGGAGGCGAGGTTCCCCTTGCAGGGGCAGCAGGGGCTACACAAGGGCAGTGCAGACTGCACAGCTGGCTTTCTGCCTTGGTCAGGGGTTTTCAGAAGTGGGGGGACTACCCAGCTGGGCTCTGACGCCCTGGCAGATAGGCAGGCAGAGGGAAGCGCCTCTGGGCCCTGTGCTTACTGCAGAGCTAGGCTGGAGGCTGCGGAACCAAAACTGCTGTGTCATTGCGACGCTGCAGCTGTTGCCTGGGTGACGGGGTGAGTTTCCCACGATTGCCCCTGGCGGCCAGCGGGCAGGGAGAGGCAAGGGGTGTGCCGAGGCCATGATAGCCACATGGGCCCTACGGCTTGAGGTCCCGGGTGTCCACCCGCTTTCCTCTCATGTCCTGCCCCCGGATACCACTGTCGTGCAGGGTGGTGGGGATATGTGTGACTCTGGAGGAGCCCAGCCCCATTGCAGCCTGGGCCTCTTGTTCTCACCTGGGTGGTGGTGGAGTGCAGAGTGCCTGGGCTCTCAGGTGTCCAGGGCCCATGGCAAGTGTTAAGTGACAGCTTAACATGGTGGGTGGTGGAGAGTAAGTGAGCCTCTTGTATGCTGCTGAGAGGCTTGAGATCCCCGAGATGTGAGGTCTCTCGTACCCTGCTGGGGGGGGAGTCCTCTGAGGGCTGGACATAGAGGTGGTCCTGCTGGCCCTTAGCCGTTCTGCCTGAGTAAGGCTCTGTAGAGGGAAGTCTTCCCTCGTAGGAGACCCAGCTCTCCTTAGCGCTCATCACCAGCCTGCCAGGGCTAACCTTCCCCAATGATTCTCTTGCAG
Seq C2 exon
CTCAACTCACCCATGAACCCCGTGAGCAGCAGTGAGGATATCAAACCCCCTCTAGGCCTCAATGGCGTCCTCAAGGTTCCTGCCCACCCCTCAGGAAATATGTCATCCTTCACCAAGCACATCTGCGCTATCTGTGGGGACCGCTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009446:ENSRNOT00000012892:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.944 A=NA C2=0.549
Domain overlap (PFAM):
C1:
PF118253=Nuc_recep-AF1=PU(69.8=91.0)
A:
NA
C2:
PF118253=Nuc_recep-AF1=PD(28.4=64.7),PF0010513=zf-C4=PU(15.7=21.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]