RnoINT0130043 @ rn6
Intron Retention
Gene
ENSRNOG00000009446 | Rxra
Description
retinoid X receptor alpha [Source:RGD Symbol;Acc:3610]
Coordinates
chr3:6284287-6288243:+
Coord C1 exon
chr3:6284287-6284456
Coord A exon
chr3:6284457-6288113
Coord C2 exon
chr3:6288114-6288243
Length
3657 bp
Sequences
Splice sites
5' ss Seq
TCAGTGAGT
5' ss Score
7.68
3' ss Seq
ATGTCCTTCCTCCACTCTAGCCA
3' ss Score
7.92
Exon sequences
Seq C1 exon
CCGTGCAGGAGGAGCGGCAGCGAGGCAAGGACCGGAACGAGAATGAGGTGGAGTCCACCAGCAGTGCCAACGAGGACATGCCTGTAGAGAAGATTCTGGAAGCTGAGCTCGCTGTTGAGCCCAAGACTGAGACATACGTGGAGGCAAACATGGGGCTGAACCCCAGCTCA
Seq A exon
GTGAGTGTCAAGATGCTCACCTGCCTCAGTTTCCCCTTGTGCTTACCCTCCTGCTTGAACAGCCAGCGAACCCGAGCCCTTTGGCTGCTGTGGCGTTTGTCCCCACCAGTGGGACCTCTGTCCAGCTGGTGACCCTGTGACTGGGGGGAATATACCAACCTTCCTGCTGGCCTTGCCTGTCTGCCTCATCCAGATACTCAGCAGGGTCCAGCCCAGGACCAACTGCCATTGTGGGTCTTGGCTTACACGCACAGTGGGGCTTGAGCTCAGTGCAGGGGAATCCTGCAGAGAAGCTATGAGCAGCTGAACCCGGGCAGAGCAGCAGTCGCTGGGCTCCAGGCTGGCTCTCACCAGAGTACGGTCACAGGGAGACAGACGTTCTGGACCTCCCTCTCCTACCCACTGCTATGAGGAGGTGGAGAAGCCAACAGGGAGGTGCTGAAGCAGAAATGTCTCTTGGCCCTTCAGCTAGTCATCCTCAAACTGGCCACCTATAGGAATGGCCTAGGCAACCACTTTCCCATCTTCCTGTACCACCTGCTACCTATAGCTGCTGTGGCCTCCAGACAAAACCGGAAGGGCCACAGTGTCCACTGCTGGCCCTTTTCCTGACTGCAGGGTCTTAGTTTCAGATCTTTCTGGCTTCCATGCCTGTTCCTGGACTTTCATCTGAACTCTTCCCCGAGCCCTCCCTCCCCTGCCTCTGCTGTCACTTCATTGTGACATTGGCCAGTGTGGGCTTGTTTGGGTGGGATACCCCATTTGCCCGAGGCCCCAGTCACAAGGCTGTGGCTGTGTCCCAGATTATGATGTTTCTTGTGCAAATTCAAGAACAGGGCCTTGCGGGGTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTTGGTCCCCAGCTCTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAACAGGGCCTTGCACAAACCCACAAGCCTCATGTTGTCTTAAGCACATGGCCCAGCTATGTCTGCCCTGTATGTGCTTTTTCTTGATATCCTGACCTCATCTGGATTTCCGTGTGGGCCTCAGATCTGTGACTAGAGTCTTGCCATTAACCGTTGGACACCCAGTCCAGATAGACCTCAAGGAAGGCCCGGTCCGTTTCTCCCTCTGAAGCAGACTTATGCTGGTCTTCTTGAGTCTTAGTGCCCTCGTCTCAGCCTGTGGCCCTGGTTGTTTTCCTTCAACTCCAGGTGTAGGGCAGGGGGATAGTGAGCTATCCCAGGAGTCAGTGGGGTGTCTGAGCTATGTGGGGTCAGCACTTTTGGCCTGTCCTAGGGGCCCAGGCATGTCTCTTCCTCTCTGTAGTCTCTCCCCTTGTATACTTGTGAGGACCTGTGACCCAGAATTCTTGTGTCTAATCCCAGAGCTGCTGTACTAGGGGCAATGCTGGTAGCCTTCCTTGGCGGACCCAATCCTGGCTCTGTTACCACACCTGCCAACGGAGACCACAAAAAGCCTTGCCCACTCGAACCTCCCCAGCGCTCTGGTTGGAGTCTGTTCCCTAAGCCCTCTTATCAGTCCTGCAAGGGAGAGGAGAGCAGCATCAGGACTTTGGAATAGGACCTGAGGGTGGTTGGCTGGGGTGTGAAGGGGGGGACTAGGGTCTTCCTCTATCAAGTAAGGCTATTGTTGGGAATGGCCTCAGTTGTGGCCTTTGCCGCTTTTCCATGAGGGTTCAGGTCTTCAGAGATACGCAGTGGGAGGTCAGTGTCCTGTGACTGGCCTTGACTGCTCCATACATGGACCTGGTGGTCTTCCCTCACAGGCAAGCTAAAGAGGCTGGACAGGCAGCACCTAGCCACACAGATGGGCCGCTGGCTCCTCGGGCCCTGCCTGGGTGGGCTTGTGACCACGCCTTGCTGGGAAGCGGTAGCTCATTAAACGTCTGCAGTGGAGTCTGCTGAGAGGAGTGAAGCTCACAGTGGGATAGAACAGGGCAGAGCCAGGGCATGCTCAGTCCTCCCTTCCAGACGGCCCTCCAGTGAGAGCCTGCAGGCCTCGGGCCTCATACCTGTATAGCCCCCGCCTCCTTCCTTCTGCTCTAGCCTGGTGCCCAGTCCTGGCAGATGGCATGTGTGCACGTGGCCGCAGAGGCCACAGTCAGCCGTGGAATAATTTTTGAGCTCTTTTGCTCAACCATAGTAGCATTGTGGCAGTGGATTCAGAGGGTGGCCAGGGAGAAAGCTGTTTCAGGCAAGGCAGAGATCACAGGGCTTGGGCATGAGGCTTGTTGTCCGTGCGTTCTCACAGCCGGCCTGGGGCCCTCACTGTCTCCTCTCTTTGGGCTGCTCCTTGGTAGATGGCAAGTGAGGAAGACATCCATGGAACAACCCCCTGTGGCTGAGAGACAGAGCCAGGCTGCAGACAGCCTTCATGCTAAACAGAGTCAGTCCCTAGTACCTGCTGTGCTGGGGCTCTGCTGGCCTCTGTGGCTGGGGTATGGCACCCATTCCCTTGGACTCTGTCCTGAGGACCATGTGCTGACATCACCTGTCCTTGCTGCCCCGGGCTTCCCCTGCAGCCAGTCCTGCCAGGCCAGTGGTGCGAAGCTGACTTGTCAGTGCCTTTTCACCGAGCGCTTCACGGGCCCTTCACACGGGGCTGGGTGTTTAGACTGAACGTCACCGCTGAGCAGATGGTTTCTGTCAGCTGAAGCCCGTTAAAGCCGGCCATTCTCTCCTTATCCGATGCTCAGCCACTTCTGTTTGTAAAGCCCAAGAGTCCTGTATCCTGTTCTCGGGTACTCTTAACCCATCACACCCTGAAATCAGAGGGCCCTGGCTCCCCTGCCAGGCTCTGGGATGGGCTTTTCAGCCTACTGTGAGGCCCACCTGAGCACCTCACCTATGGCAAGGACTGGTTGCTCCTCTTCTGGGCAGAACTTTCTGGAAGGCTTCTAGTGACATCACCTCTACCTACGACTTGGAATCTGGACCGAGCAAGGACCAGCCCTAAGCTTGTACTTGCATGTTTGATAGGACTTCTCTCTTCGGTGGGCTACTGTTACCTTCAGAGATGGGGTCTGGCCCTACCTCAGCCCCCTCACCTGCCTGTTAAATGCCCTCTATCATCTTCCCTCAGGGTCTTCCTCTCAGGGCGGGGAAGACCTGATGGGCGGTGGTGCACATTGCCAGTGGCCTCCATGGTACAGATTCTGTTTTCTTCAGCCATTGAGCTGTGTGACCATAATCTGTGTGGGTGGGACCCAGTCAGGCCGTTGGCAGTGCTGACTCTCCCCTTCCTGCCTTTCCCGCATTTGGAGGTTCCCCAGTCCCCTAACTTGGGACTCCTGCCAGCTTCAGGTCAGCCGTGTCTTCTAATCTGCTTTTTTTGATACATCCCTCTGACTTCGAGGCTCTTGCTTCTTCTGATGACCCCCGCCGTGATACTAGTCCAGCTCCAGTCAGCCAGGGTCATTCCCCCATCCCTGGTACTATGGGTGGATCTCTTCTTCAGAGTCTTTCACTGTGCCAGGTCCCAGATGCCAGAGTTTGGGATGCAGATTCTGGAACTCAACTCCATGGTTTTTTTTTTTTTTTGGCGTGGGCTGAGGTTGTTCTGCCGGGGTTATCAGAGGTGTGAGGCTTGATCGATGTCCTTCCTCCACTCTAG
Seq C2 exon
CCAAATGACCCTGTTACCAACATCTGTCAAGCAGCAGACAAGCAGCTCTTCACTCTTGTGGAGTGGGCCAAGAGGATCCCACACTTTTCTGAGCTGCCCCTGGACGACCAGGTCATCCTCCTCCGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009446:ENSRNOT00000012892:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.579 A=NA C2=0.114
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=PU(4.7=15.8)
A:
NA
C2:
PF0010425=Hormone_recep=FE(22.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
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]