RnoINT0130044 @ rn6
Intron Retention
Gene
ENSRNOG00000009446 | Rxra
Description
retinoid X receptor alpha [Source:RGD Symbol;Acc:3610]
Coordinates
chr3:6288114-6290106:+
Coord C1 exon
chr3:6288114-6288243
Coord A exon
chr3:6288244-6289973
Coord C2 exon
chr3:6289974-6290106
Length
1730 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CATGTGCCTCCCCTCCCCAGGCT
3' ss Score
10.97
Exon sequences
Seq C1 exon
CCAAATGACCCTGTTACCAACATCTGTCAAGCAGCAGACAAGCAGCTCTTCACTCTTGTGGAGTGGGCCAAGAGGATCCCACACTTTTCTGAGCTGCCCCTGGACGACCAGGTCATCCTCCTCCGGGCAG
Seq A exon
GTGAGTAGCCCGGGCAAGTGAGGCTAGAGCGGGAGGCCGCCGGTGGTGTGGTGAGCTCCGGCCCACTCCTGTTGTCTAGAGCGACTTTTCCCTTCCAGCTAAGAAAGTCAGTAGAGGCTCTCCTCAGGCTGCCCGCCGGGTCTGTGCGACCTCTGCAGCCGTGTCACCTTCTAGCTTCAGGTCTTTTTCGGAGCAGAGGTCTTGATACAAGTGTCTGGACCATAAGAGTATGTCTCTGTCATACTCAGCCGAGGGGACCATTGGGGAGGAGTGTAGCCTTGGAATGTGGGGTGGGGCTAGGTCTGCAGGCCGCCCTGATCCTTATTTATTAACTGGGCACTGGGGCACGCTGACTGTTGCCCAGATTGCACCAAGTCACCAGTAGGGGTGCTAAGACTGGGAGCCTTACTTCTCCACCTGTGGAGAGAGAGGCACCTGCAGCTCTTGCTCACTGCAGAGCTGTGGTGACGGTGGACACTGCCTCGCTCTGGTGCCCATGCTGTCTTGAGGGGCCTGAGCGCCCTGACTTGCTTTGGTTTTCTGCTTGCACCAAGGGGCTCTCAGCCTCAGTCCACCCCTGGAAGATAAACTGAGCAGAGATGGAACCCTGTGTATCATGGAGTGTACTTAGTTGGGGCGTGGCCTTCCTGCTTTCCCCTTGAAAGGATCTCTCGGTGGGCATGGGTTGCCGAGATGAACAAGATGGATTCTGCCATGTTGGCCTCTGCCTAGGTGGGCTTGTGCCCCATTGGGATACGGCATGTGACCCACTTTGTGAACACAGGGCTTCTCTGAGGCTGTGGGACGCATTCTGTCCGGGAGAAACACCACTGTCTGGGTCTTTACCGCAGTGACTGTGGGCACAGCAAAGTCCCCTAGCCTTCTAGCCTTGGACCAACTGTTTGGGCGTTTTAGAAGTCCTTGCCACCGAAGCAGGCCAACCCACGTGGAAGGAACGGCCGGCCCTGGGATGTGGCCTCAGACGACCTGCTCAGCGTAGGGTTCAGGTGCCTAGATATGAGGCGAGGCAGAATTGGCCACTCGTACCCTTGCGGGGTCCCCAAGGTCACATTCCTGGGGGTGATCTCCCCCGTGGCAAGAAGCATGTCCTGCCCCACCTCTCGAGTGCTGACTGCTTCCGTTTACTCTTGTAAAATGTGTCAGCGTGCTTGCAGTCATGGTATGGGACCAGCAAGGCCTGGGATTTCGGAACATGGAGTTTCTGGACTCCATGTGCTACCTCGTCAAGGAGCCCCTGGCTGTTTGTGCAGAGTCCTCTTCTCTTCCTCTTCAGGGCCCCCTTTTAGTGCTTCCGTAATAGCTCGAGCCTGGGATATGTGGCATGGCGCCCGTGTCTCCAGGGCATTGTGCATGGTCCAGACTGGCAGCAGCCCTCCCTAGCTGTCACAGGGGAAGTCCTTGGGAGGTCTCTCAGCCACTCTGAGGCACACGAAAGAAGCTTCGGTGCCCTGCATTTGTACGAGAGAGTCCTTGGGGTGGAACTTTCCAGGCAGGAATACTGGTAAACTGTGTACTTGACAGAAGGAAGAGGTGGAGTTCACGCTCAGGTGCCCAGGAACCTTTCTCTAGGTCCACTTGCTGGGCTCCCACTTAGGAACCCGAGATGAGTCTGGAACACGCTGCTTCCGGAGCTCTGGTGTGGGTGAGGGGAAGGGACAGTGATGGGGGTCATAGAAACAGCAGAGTGACCATGTGCCTCCCCTCCCCAG
Seq C2 exon
GCTGGAACGAGCTGCTGATTGCCTCCTTCTCCCACCGCTCCATAGCTGTGAAAGACGGCATCCTCCTGGCCACCGGCCTGCACGTACACAGGAACAGCGCTCACAGTGCTGGGGTGGGCGCCATCTTTGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009446:ENSRNOT00000012892:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.114 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(22.4=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(22.9=100)
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:
CCAAATGACCCTGTTACCAACA
R:
CTGTCAAAGATGGCGCCCAC
Band lengths:
263-1993
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]