RnoINT0130042 @ rn6
Intron Retention
Gene
ENSRNOG00000009446 | Rxra
Description
retinoid X receptor alpha [Source:RGD Symbol;Acc:3610]
Coordinates
chr3:6277183-6284456:+
Coord C1 exon
chr3:6277183-6277362
Coord A exon
chr3:6277363-6284286
Coord C2 exon
chr3:6284287-6284456
Length
6924 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
TGACTGTCTCCTGTTTACAGCCG
3' ss Score
9.65
Exon sequences
Seq C1 exon
GCAAACACTATGGGGTCTACAGCTGTGAGGGCTGCAAGGGCTTCTTCAAGAGGACAGTACGCAAAGACCTGACCTACACCTGCCGTGACAACAAGGACTGCCTGATCGACAAGAGACAGCGGAACCGGTGTCAGTACTGCCGATACCAGAAGTGCCTGGCCATGGGCATGAAGCGGGAAG
Seq A exon
GTAGGCTTTCAACACCCTCCTGCCCAGCCTCAGACCCAGGGCCTCTGTTGTCCCCTCCCTCGGCATTCTTCTTGTGGAGGGATTTGACTACAGAGTCCAGTCCTGCGTTTTGCAGTTTGCCAGATTCTGGTATAGCCTGGCCGGTTTCTTTGTGAGCCTCCTGCTCAGCAGAGCCCCTGGCCTGCTGTCTGGATAGCTTGCCTTCCTGCTAACCCTTCCCCCAACCAGACTTTCACCGAATGCTTGCTGTGTGGCTAGGTCTTGGGAGTTGAGAATAGACAAGATAGACCAGGTCTGCCCCACTGGCGGCGTGGCCAGCAGGACAAGGACTGAGCAAATACTCCACTCCAGCATGTGTCAGGGAGAGATGAGGCTCGGAGACCAAGCACTGAGCCCGAAGCGAGCAGAAGAGGCTGGAGGCAGAAGTAGGGGCGAGGAAGGGGGGAAGAGAGGCCCGTGAGATGAGGCCCATTTGGGTTGGAGTGGGGGAAAGGGCCCCTCGAGACCACCAAAGTATCTCCCAGAGCCTGTCGAATGTGAGGGTCGTCTTCCCTTCTCAAGGCCACTTCCGGTCTCATCCCTGGCAGGGTTACCTGTCAGCCTTCAGGTCCTCTGAGGAGCAGGATTCTGAGTCTGTTTTATCAGCAAGATGTATATGCACAAGGTAGAGAGGCTAGGTGCCATGACAGTTCAGACGACTCCCCCAGAGGTCCCAGATGTCAAGCTGCATAGCTAGACCTCCCAAGCTACACTGTGCCCTCCTGACCCTACATGTCGGACAGTAATTCTCTGGTTTGGTCTGTCTGTCTGTCTGCATGGGTGTGTATATGTCTGTCTGCCTCCTGCCTGCTGTCTGTCTGTCTGGGTGTGTATATGTCTGTCTGCCTGCCTGCCTCCTGCCTGCCGTCTGTCTGTCTGTCTGGGTGCCTGGGTGAGGTTTCTTCATCAGTTTTAGGCTCAGGCCTCACAAGGCTGGGCATTCTCTGAGGCAGGGTCTACTCTGTCTCCAGCACTGTCCCTCCAGCTTCCTCTGTCTGGGTTGTGCACAGGGACCAATTCCTACTGTATGTCCTACCCCTTCCTACCAGCTCTTCAAAGGCCCCTGTCCAGGACTGAGCTGAGTAGGACCAGTGCTGAGGTCTGCTTTTCTCTTCACAGTGACCCCTTCTTTTGGTACATTCTGACCCTCTTGTTCATGAGGAACCCTGTGCTCCTGTGGGATTCTTCCATGCTGTGAGGTCAGGGGTGCAGGGGTGCCAGCAGTCTGGTCCTCATTCCCAGTGCCGGTGGTAGGGCAGTTCATAAAGAATTGTATACTGTGGAGCTGGAAGTGTTGCGAATGTCCCAGTCAGGGCATCCTGACTGGGCGCACGATCAGAGTGTAGAGTTCTTTTACATCTGACCTTGACTTTGCTAAGAGGTTTCCGCGGCCATTAGGGCCCAAGTCTTAACACCGTTGCCTATCTGAGCTAGACCCCAGCTTCTGGCTTCCCCCCTACTTTCTCTGTAGTTAGAAGGTAGAGGTGGGGAGTGCTCTGCCATTAGAAGGAGTACGCTGTCTGTCCTGGGGGTCATGCCCTCGAGGGAGCACTAACTGGGAGTAGTCAGTATATCGCATCCTCTGGAGGACAGGTGCTTGAGTGGGCAGACCTGGGGTGGGCCGTGGACCCGAAAGTGACCACTAGATAAACAGGTAGGTCCCTGGCTTTGGTCACATGAGCTTGGGAGCCTGTACCTGACCCAGACTTGGGTGGTGGACATGCTCTGTCCAGATATGTCCAGATATGTCCAGGCTGACACCTGAGCATGGACCGATTAGGTACTGTGTGGCAGCGGAAAGGAGTCATGTCCGTGAGAGCCAAGGCTACCAGCAGACCTGGCATGTGGTGGGCACTGGAGTTCCGGCCCCAGAGAGGGACTCTCTAGCTCACATGACCCCTTCTTCCATTGCTCCCATGGTTGCCCTTGGGTGCTGGTGTTCAGACCCCAGCTGCCTGGATTTCGAGAGGTATGGTCATTGTATGTGATGTCCCCTAGTCCCAGTGTCACAGGAAGGGAGGCTGGAGCTGCCTAGGTCCCACTGTGTACTTCCTTTGGGTGGGGCACGGAGCAGCCCCTGTCCAGTCCTTGCACATAAAATGCTTGTCCCCCATGCCTGTGCCTAATGCTAATGTCCTGCACAGAAGTAGAAGTGGGGTGCAGAGAAGAGGACTCCACTGCAGCCTGCTCTGTTCCTTGGGCCACCCTGTGTTTGTGACACCTGAGAGACGCTTTACCCATTCCTCTGGAGAGATGCACCGAATCCCACCCCATGCCTCTTTGTTCCAGCTGGATTTATGAGTGTTTAGTTTAAGCCCTGTGAAGCCTTGTCTTGCCCTAGACACAGAGGCCATGCACCTTGGCCCCTTGGGCTGCACAGCATCTGTGTGGCAGGTATAAGATGTCTGGAGGCCCTCAGACACTTACAGCTGAGGCACTGGGCACTGGGGGAAGGGACTTTTTCTTACCTACCTGAGATCTGTCATATTTCCCAGTGTCTGTAGCCATAGTCCACGGCCCCACTCTTGAGATGGTTGGCCTTAGAGCATCCTGGGAACCTACCATGCGGGGATCTCTTGAGAGGATTCCCAAGGGCTGGTCCCCACTTCTGCCTGCATTTAGGTATTGGACACTGTCCCCGTCCCACCCTGGGATCTGGACCAGTCCCCAGAATGAATTCGTATTCGTTTCCTTCTGCTCTCCTGGGCTAACCACTGGGAGGAGAGTTCTGTGAGCAGTGGGTGGGGCTGTTGGCTGTATGAGTTGGATGGTCTGACAGCCTTTGGAGAAGCTGTGGGGCCAATTGCCAACCCAGGGCCTTTGGCCCAGAGAATTCAGGACGTGCACCATCGGCTCCCATGCTAGCTCAGCCCCCAAGTGCCCAGCCCCGGCGGGTAGCAGTCATTAAGTTGTGGAGCCTGAATCTAGTGATCTCTGTCTTCCAGGCTTGGTCACACATAACCCTGGAAACTGAGGCTGGTGTAGAGGTGCTGTGAGGAGGGAGCTGACCACAAGAAGGCTATGTCTCCCTGTGGGGTGGCCCTGGCCTGGGAAAGGCACCCTGTCTTCAGGCTGATGAAGGATACTGCGGGCTGATAGCATCTATGTTGGGCAATAGCAGGGGCCTGCATGTGCAAGCAGCCACGGGGACTTGTTTGGCAGCATTCCCCAGCTGGGGGTAGGCAGTGCCCTTCTCAGGCTGGGCCTGGGCCTGGGCCTGTTGGCTGGGGCAGGTGGTGGTAGGGCTGGGGGGCCTGCAGGTGTGATGCTCTGCAGGCTGGAGAGGCTGTACACTGCACACTGCACACCCCATCCTCAGCTCCCTTCCCCCGAGACCTCTTAGCATTTCCTTCCTGACTCTCTTAGCTTCCTGCACCCTGTCCTCTGGCTGTGGAGCACTTGGGTGCGGAAATGGCAGTTTCTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGCATGCATGGTGTGGTGTGTGTGTTTGTGGTGTGTGTGTGGTGTGGTGTGTGTGTGTGTGCGCATGTGTGTGTGCATGTGCTTGTGCACACAGACAAGGGTGAGCCCACCGTTTCTGCTGTGGGGAAATGGCCCTGGCTTAGTTGTTTCTCTAGGTCTATGACTTTACCTCTCTGAGCCTAGTGTCTCCATCTGAACATGGGGCTCCAGTAAGGTCCCTGAAGGCTTGTTGGTGGGACAGAGCAGAAGAGCTCAAGCTGGTAGTAGGATTGGAGCGTGGCGGCCACAGTGTATTTTTGTGCTGTATCTGTGTTTGTCCATGCGTGCATGTCTGTCCGTGTCTTAACTCTTCTTGCGACTTGCCCCAGACTTGTCCTTGAGAGAGGGAATATCATACCCTCAGCATGGGACCTTGGGAAGAAGCCACTCGCTCTGGCCCAACCCTGCCTGAGTATGAAGAAGGGGAAGAGGCTAGTGTATGTTAGTTGAACCTGGTCCTGCCTATTTTACAGACCAGCTCTGGGCTTTTAAGGAGCAGAGGAAAGCTACAGTTTCTGGCAGAGTCCCAAACATGGGAAGCACTAGGATCTGGGATACCCATTTACCTCAACATCCTGTTCAGGTCCCTCAGTTGTGCTTGGGCCCAGTGGCTGAGCAATCCCCACACACTCCACTTTTGACTGTGTCCTAACTGGGGATCCCGGTGTGTCGGAGGAGGCTCATCTCCTGCTCAGCCTGCATTGGATCTTGGGAGGGCTGAGCCACGGCTTCAGGCACCACCACAGGCTGAGGGAACCTCAGTGTCTGAGGCAGCCGCCTCCCCCGCAAGGCCTGTGCGGGCTTGGAAGGATAACGAGGCTCTGTATTTACAGACGCCTCCCGCCCGAGGCTTCCCGGCGCCAGTGGAGCATAAGTCAAACATGAGTGTGTCTAAAAGGTGATTGAGCTGGCAAAACATAAATCCCCCACTCCCTCTGCCCCCTCCACTGCCTATAAATAAAACGATAATATTTATAACGATGCCGCCCTGAGCTGCTGGGGCCTTCGGAGGCTTCAAAGTGCTTCACAAAACATTTGCTAATTAATTCTCAGCTGCCCCCGCACGGGAGGCAGGTGTGAGGAGCCCCTCACCCGCCCGCCCGTGGCCAAGCTCTCAGGGATAACTGGCTGCTGTGAGGGCCTGCACTCTGGGCTGCCTCCTTCTGGGCTTCTCACATCCCAGGGCTGTCTCTGAGAGTAAGGAAGTCCCTCACTGGAGAGTGAAACTGGGCCAGCAGGGTGGGGCCCAGCCTGCTCAGGTGCTTCCTTCAGGGTTCCCTGGAGGGCAGGCTCCACACTGACATTTTACAGGAAGTGGGGTACAGAGATGCTAGAGGAGTTGCCCAAAGTGCCACAGCTGCTCGAGGCGGACCTCTCACTCCAGAGCCTGCAGTTTGCCTTGGCACTTGTCTCTCTGAGTCTGATTTTCCCGTCTGGGAAGGTGAGGCCGTTGAATTGACAGTGTCCTAGCCCAAGACTGAAGAGTTTTGTCACCTGGCTTTGAGATGGGGTGGGGGTGGACGGTTGCCTGGCTCTGGCTACAATTGGTCTCTTCAGATGCCGCTCAGTGGGGCTGCTTAGCATTAGCGGACTGAGGAGTCTCTAGGCCCTGTGCTAGACCCCTCAGTGACTTGTGGAGTGACCCTAACCCAGATGCGCTGGCAGCCACATGAAGGGCCCATAGGAGCCCAGCTGGGGAGGGATAGAACCGGGCAGATTTTTGCAGCCCTTCCCCCGTAGACTGGGCACCATCTGCCCATGGCATTCAACTCTGCACCAGCCCCAACCTGCTGTCAGATTTTCCAAAAGAGCCAAGCTTGCAAAACACCAGCCTCTGCCCAGTTCCTCAGCCCAGCTGATGTTGTGCAGGCATCGGACCAGCCTTCCATCCGTGGCGTGTTCACAGGTAGAAAGTCTCTGCTACAACCAGGCCATTGAGATTTGGGGGAGCTTAGCCCCAGCATGGGAGAGCCTCAACTGGATGGCGTTGGTGGGCCCAGCAAGGATCAATAGCCAGGGGCACTGAGAACCGTCACAGAGCTTCGGAAGAAAGGGAACCACTGGGCTGAGCATTGCAGTGGGAGCCTGGGAGGAGTGAGGGGAGATGGGCACAGAGAGAAGGCTGCTCCCTGGGAGGTGGCCGCCAGCAGCTCCAGGTGGTTGAGGAGGCCGGTTGCAGCGTGCGAACCCCTTCCTCCTCAGCCCTCCTGTGGGCCTTGTGTTTTACTCTGTAAGCCATTCGTGGGCCAGGAGGTAGGTCTGGCTGTAGAAGAGGAGGCTGGTGCTGCCCTGCTCTTGAGACCCTGAGGCTGCTGAACTGTGTCCTGCCACCTACGGAACTCAAGGGTTAGGAGAGCTCTGACCAAGGTCCTGAGAGAGCAGCACCAGGCAGATCCCTTGGGCCACACTCTTTGGAAAGGCGCCCTTCTGGACACTGGTCTGGAGAGGAGACCACCCAGGGCTCCACCTAGCCTGCTGCAGGAACCCAGAATGGAGGGAGGGGCCTGTTGGTGTCAGAGTGTGGGCAGGACAGAGGAGAACAGGTCCACAGGAGCTGTTAGAGGGAGGCAGGAGGATAGAGCATGCTCTGCTGCTCTAGCCTGAGGCTCCTCACTGGACCTGCAGGCTGGACAGCTGTGGGAGGAGCCAGCCTGCCCAGCCCACCGGCCTTTCCCTTCCATGCTGCCCCTTACCATCCTCGAGGGCCAGGCTGCTCACAGCTATCTGGGGACTGTTGTCTGGGGTGTGAATCAGGGTGGGCAGTCCCAAGGCCCGTGGCATCCTGGAGGAGTGGGGCCAAGCTATGGGCCGTGTGAGGGTGGGGTGCTTCTTGGCCGAGGCAAGCACAGAGAGCCTGGGCCGTGCATCTCTGACTGTGACTGTCCCTAGCTCTGCCTTATCACCTCAGTGGTCACCTGTGTATCACAGTCACCACCCCTGCTCCTGATCAGAACATGCCCTGTACTCTTCTAGACATTTTTGTAAGTCGTTTCTTCCATTGAACTTTACTCCCTCCGTTAGATCCATTCCTGCTTCTTCCAGGAAGTCTTCTTGGATTTCCCCACATCCTCAGACCACCAATGTCTTGAAAACCCATGTTAGAATTCCTGTGACCCATCAGCTCCAGGAAAGGCCATCTGCCTTGAGCTCAAATGGGCTCTGGTGTGTTTCCATTATTAGCTGGGTGTGTTCAGGGCATACAGCCACCCAGTGGCAAGGTACAGGCAGGTCTTAGGCTGGGCTCAGCCTGTGTCTCCCTCAGCTGGCCTTGGAGGGGACTCCAGGACACTGCCTTGGAGCTAGCCCTGCCTGTCCCTGAGCATGTTGTGGATGTCCTAGGAACTGTGGGGACTGGCCAGCCTGGGTGACTGTCTCCTGTTTACAG
Seq C2 exon
CCGTGCAGGAGGAGCGGCAGCGAGGCAAGGACCGGAACGAGAATGAGGTGGAGTCCACCAGCAGTGCCAACGAGGACATGCCTGTAGAGAAGATTCTGGAAGCTGAGCTCGCTGTTGAGCCCAAGACTGAGACATACGTGGAGGCAAACATGGGGCTGAACCCCAGCTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009446:ENSRNOT00000012892:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.579
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(82.9=95.1)
A:
NA
C2:
PF0010425=Hormone_recep=PU(4.7=15.8)
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]