RnoINT0130045 @ rn6
Intron Retention
Gene
ENSRNOG00000009446 | Rxra
Description
retinoid X receptor alpha [Source:RGD Symbol;Acc:3610]
Coordinates
chr3:6289974-6292058:+
Coord C1 exon
chr3:6289974-6290106
Coord A exon
chr3:6290107-6291966
Coord C2 exon
chr3:6291967-6292058
Length
1860 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
GGCACTTGCTTTCCCCGCAGGGT
3' ss Score
10.49
Exon sequences
Seq C1 exon
GCTGGAACGAGCTGCTGATTGCCTCCTTCTCCCACCGCTCCATAGCTGTGAAAGACGGCATCCTCCTGGCCACCGGCCTGCACGTACACAGGAACAGCGCTCACAGTGCTGGGGTGGGCGCCATCTTTGACAG
Seq A exon
GTGGGCTGGGAGGCGCCTTCTTTGATAGGTGGGCAGGGTAGGTACCATCTTTGGTAGGTAGGTGGAACGGATGCCATTTTCAGTGGGTGGGAAGAGCGGGTGTCATTTCCAACACGTGAGTGGTGTAGCATCGTCTTTGATGGTCTGTGGGTTGGTAGGCTAAGTATGGATTGTGGTCAGCAGGTAGGTGAGGTGGGTGTTCTTTTCAATATTCGGGCCATCTCGAATGGGTATATAGGGCAGGGACTATCTTAGACAGTTGGGGACAGGCCCCTTAGTCTCTTCCTGCTCTGTTGGACATAGCCTGTGTGTAGGAAAAACATTAATGTGAAAAAGGCAGGCCCGACATATGGAGATGGCTGTCTGTGCAGTCCGGTGTCAGGGGGGTTGAGGCCACAGGCAGCCCTCTTCCTTTGTGAGCTGAGTATCCCTAAGTATAACAAAGACAGGTTACGGCACTGGTATGGTTCTATAGTGTGAACATTGGGCACACCTCAGCCATAAGCACCGTCGTCATCCCAGACCTGTGCCCTGATGTATCACTGAATAACTGGTGTTTCTGATCTGCTGCTACTCACGCCCCCAGTGGACCTGGGTCTGGAAGGCACCTCTGCACATGCCTGAGCTGCTTTTAACACACATGCTCAAAGGAGCAGGCTGCCTGGAGTGCAGACACATGCAAAGGCCGCCCGGCCCCAGCCAGTTACGCTTCTGCCATGCTTGCCTTACTTATGCCCACCAGCTGAGGGACTGCGACTGCCTGTCCTCTGTCTGGATGCCCAGCCTTGGTGTACAAGCTAAGGGCCCATGCCAAACCTCAGTGTCCTGGGGACCTGGATGTCAGTTGCTGCCAGCTGAGGTTGGGGGTTTAGGGATGGTGCAGGGCCGTAGGGCAGTGAATGGGAATGAGCAGGCCTATAGGAGGAAGTGGGGAGAGGGTGAGTCCCTGAGCTCCTGAAGTCAGAGGTGAGCAGAGCCACCCACCAGTACTCTGGGACAGTGAGGACAGTACACAGACTGAGCTCTTCCCAGGTAAAGGCCAAGTGGAGCACACAGGCAGGCCGTCTAAGTACAGAAAGGTTTGTTGCTGCGTGGGAGACAAAGGCTAACCTCAGCTCACTGCCAAGCTCTCTGCTACAAGCCTCTGACAAGCTAACATATGGGGCCGCTCCACAGGGGAAGGCATTAGGGCTTAGCCTTCCGGGGTCCAATTTTGGGAGGTAGAGCCAGATGCCAGCTTGCAGTGAAGTGATGTACTGGGGGCGTTATACTTCTGTCTTCTGGGGACGCTGGTTGGAAAGGTTCTAGCTTACCCTCATTGTCAAAGGGTGAAGTCTGACCCTTGGTGTCAGGGCTCCTCCTTGCTGCTGAGGTCAGAGAGACTCTGGTTCAAGTGGCTGACACCGGAGTGGAGCCTAGGATTCTTCCAGATTCCGCACATGTCGAGTGGGCTAAGGACATGTGAAGGCCCTTTGGAGGCATCTTGCTGAGGAAAGGTGATATCCGCTTATGGAAAATGACTTCTACCAAGAGGCTTTGTCCCAGGGAAAAGTCTAACCTGGAGCTAAAGGGAACAGCTATGAGTGCAGGGCAACCTGGGCTGGCCACACAGCAGGAGATCTTGTCTCAGCTCTCCTTAGGGTTCCTCCTCTGGGCTCAGATTCCCAAACAGCGCTGGGGTAGTGGAGGACACCATCCTCCACAGAACTGAGCTCATGGCGATGCTTCCTTCCTGTGGACGTGGCCAGGCCCAGTACATCCAGCTATTCCCGGTCTACCCTGGGCTTCATGAATCCAGTGGATCCTCCTTGGTGGGGCCCTGGTAAGGACGTGTCTAACTGGCACTTGCTTTCCCCGCAG
Seq C2 exon
GGTGCTAACGGAGCTGGTGTCGAAGATGCGTGACATGCAGATGGACAAGACGGAGCTGGGCTGCTTGCGCGCCATTGTCCTCTTCAACCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009446:ENSRNOT00000012892:7
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=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(22.9=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(16.1=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:
GCTGGAACGAGCTGCTGATT
R:
GGGTTGAAGAGGACAATGGCG
Band lengths:
223-2083
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]