RnoINT0130047 @ rn6
Intron Retention
Gene
ENSRNOG00000009446 | Rxra
Description
retinoid X receptor alpha [Source:RGD Symbol;Acc:3610]
Coordinates
chr3:6293427-6295908:+
Coord C1 exon
chr3:6293427-6293532
Coord A exon
chr3:6293533-6295206
Coord C2 exon
chr3:6295207-6295908
Length
1674 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CACTCTCTACCATCCTGCAGGTT
3' ss Score
9.37
Exon sequences
Seq C1 exon
ACTCTAAGGGGCTCTCAAACCCTGCTGAGGTGGAGGCGCTGAGGGAGAAGGTGTATGCATCACTAGAAGCGTACTGCAAACACAAGTACCCTGAGCAGCCGGGCAG
Seq A exon
GTGAGCTCTACTCCGTCCCCGACAGCCCCCTGCCTCTACACTTGGGCTCAGCCACACCTCTCCAAAGCCCTTCGTATGCCACAGAACTATGCTGTCCTCCTCAAGACCACCCTGGGATGCTTTTTAGGCTTTGAGCAGGAGCGAGGCAGCCCTTGGACTCATGAGCTCTGAGGACAACTCACTTTCCCCTGTAGCCCGTTGAGAGAATCGATCCATTTCCTAGCGCACAGTAGGTCCTTGCTATTCATGACTTCTCTTCTTCACTTGTTCAGTGACCCGGAAATGCCAGCACAGTGCAGGTGCTTTTCAGTTGTTCAGAGTAGGTGTCTGAGGCTGGAGAAAGCATCGTGTCTGCTGGCCTAAGACTGTCATCTAGTCATGTCCAGGTCCAGGGTGCTGGGTGCACAGTCTAGTGTTAGGCACATAGTAGGTGTTCAGGAGGAATGGTGCATTCCAAGGATTCAGTTCTGCCTCTCCCCTTGCAGGCTCTCAGTGTGCAGACTATGTGTGAGAGGGGTAGTGTGAGACGGGCGGTCGGGCACACTAACCCGTCCGTTGCCTGGCACACACATGGTTAACTGTCCACACTGCTGTTTAGCCCTCATCTGGTTTGGTTTAAAGTGAAACTTCCCGGAGGAGGACAGGAGGGTGGCAGCAGCTTGTTTTTCCTGGCTTCCTGCCTTAGCCCATCTCGCCAGCTCAGCAGAAAACAGCCTGTTCTCTGGCGCCTCTCCAGCCGCCAAGCTTCGCCTGTGCCTTTAAACTGAGGACTGTGGGGCAGCCAGCCACAAGGCTTCCTCTCTGGAAATGAAAGACATTGTTAATAATTAATGAGGCCCAGAGCCCCCTCCACTATATAGGGAGGCCCCGAGCAGAGGTCACATGTGGGACCCCAGGTCCTGTCCCCGCACCACACTGTCCTCTCTTGTCTGTCCATCTCCCGTGAGTTCCTAGACTCCTTCCCCATGCCTGTCTGTCTTTTGCCCAGGAAACGCTCCAGGGGTAGAGGAACCCCAAGGCCTCTCCAGTCCTCCCCAGGGAAGTGCTCCTGCTGGAGCACGGAATTCCCCAGTCACTGCTGGCTCTCCCTTCAGCAGGGGTCTCCACCCTGTGGCTTGTCAGTCACCCCATGCGTATTACTAAGGCTGCCCACAGATCTTTCTGATGCATCTTCCAGGACACGCCCCACTGCCCCTATAGGCACAGCTGCTCTTGCAGAGGCCTCTCCAATGCACAGAGAGACACTCATGCCCTTGCCTGCTGACATCTCTGTTGAGGCTCTCCTTGCCCATGGAGCAAGCCCACACTTGTAACTGCTCTCCTAAACCCTGTTGGGCCTGTCCTGGCCAACAGTAGTCTTACCATTGGCTCTTCCTTTCATTTCAGGGCCTTATGTACCTACCTCACCTTACCGCACCCCTACCTCACCCCTGCTGCACCCCTGCTACATCCCTGCCACACCCCTGCCCCTTGTCCTCTTTTGTCTCCAAGGAGCCTCCTTTTTCTAGTTCCCCACTTCTTCCAGAAGGATCAACGTAGGCAGCTTCCTCTGCAGACCAGACTCAGGTCCCAGGCACTGGGCTCGGCTGGTCTCCAGGGAAGCTACGAGTCACCGAGTAGAGCAGGGAGCACTCCCCGCCTCCTGACCTGTCCTCACTCTCTACCATCCTGCAG
Seq C2 exon
GTTTGCCAAGCTGCTGCTCCGGCTGCCTGCACTGCGATCCATTGGGCTCAAGTGCCTGGAGCACCTGTTCTTCTTCAAGCTCATCGGGGATACACCCATCGACACTTTCCTCATGGAGATGCTGGAGGCCCCACATCAAACCACCTAGGCCCCGTCACCCATGTGCCGGTCCCTTGCCCCGCCTGGACACAGCTGCTCAGCTCCAGCCCTGTCCCTGCCCTTTCTGATGGCCTGTGTGGATCTTTGGGGTGCAGCGTCCCCATGGTCCCAAAAGATGCATCACCATCCTCGCCATCATCATTAATGCTTGCCTTTGGCCCAGGGCCGTGGCAGAGCTGGCGTGACACCTACCCAGCCCCCTGCCCTACACCAGGCTCTAAGGCTGGTCACCCTGAGGGTCTTGGGGTACTTCGTGGGGTCTTCAGCACCTGGAGCTGCAGGAGCTGGGAGAGGGGCTTGTTCTGGTTGCTGGTTGCTGTCGCTGGTTCTCGACATGCCCGCGTGGCACCTCTGTTTGGAGTACCCCATCTTTGCCCGTGCAGAGTCCTGGTACCCAGCTAAGGGTGGGAAAGGGAGCAGGTGGGGCAGGTCATATCCTCCTGGATCATAGCTAACCTTTAAGCCTGTTTCCAAAGATACCCTGGGCTATCACCCCGAGCAGGATTCTGGGACCACCTCAAGGCCGCGTGGGCTGGAGGTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009446:ENSRNOT00000012892:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(18.2=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(14.6=56.0)
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:
CTCTCAAACCCTGCTGAGGTG
R:
CACCCCAAAGATCCACACAGG
Band lengths:
346-2020
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]