GgaINT1024261 @ galGal4
Intron Retention
Gene
ENSGALG00000002626 | RXRA
Description
retinoid X receptor, alpha [Source:HGNC Symbol;Acc:HGNC:10477]
Coordinates
chr17:7349552-7350608:+
Coord C1 exon
chr17:7349552-7349643
Coord A exon
chr17:7349644-7350502
Coord C2 exon
chr17:7350503-7350608
Length
859 bp
Sequences
Splice sites
5' ss Seq
CCGGTACGC
5' ss Score
8.81
3' ss Seq
CTCCTTCCCTCGCCCTTCAGACT
3' ss Score
9.93
Exon sequences
Seq C1 exon
AGTACTGACAGAACTCGTGTCGAAGATGCGAGACATGCAGATGGACAAGACAGAGCTGGGCTGCCTGCGAGCCATCGTCCTCTTCAACCCCG
Seq A exon
GTACGCACAGCCACCTCCTCTTCTGGCTGATGCTGTGTCCTTTGGGCTCCTTTTATTACCCGTAGAGCTCTCTTGCAATTCACTGTGTGCACTGCTGAGAATGGTGCAGCAGGGACAGCTTACAGACATGCCCCATGCCAGGGTCTGGATCCATGTGTGGCCCCCAGTGCCTCTCCTTTGCAAGAGGCATTTTCCCCTCTCTCTCTCTGGAGGAGCTTTGGTTTGATCCATGCATGCCTTCTCCCCATTATCAGCATCCCAGCTGTACAGAGTTCTGGTGCTTTAGGGATTGTTGCAAAACAGGAGCAAAAGTGGATCTAGGTCTTTAAGAAAGACAAAGGTATGGATCAGGGCAAAGTCAGAACATGTTGTTATTATTATTGTCCCCATTCCCTGATCCCACGCCAGGCTTTTCAGCAGGGTTCAGCGCTGTCTCTTGGTTTCGTTTTTCAGCTTGACTTGTGTTTTTTTTTTTTTTTCCTTCTTATAATCACCAGCAATTTGTTGTCTGCAATTTGGGATTAGCCGTATTTGGTAAAAGAAGGCAAATCTGGAGAGGTTCCCATCGTGCGTGTGCTTGGGGACAGTGACTTTGTCCCTGCTGAATCCGGGTCCTTGTCACATCATGGGGACCCTGAGCAGGGGCTCTTCTTACAGCCCTGCTGCAGGGCTCCGTGTTGGAGGGAGAAATGCCCCAAGCTGATGCCTGGAAGGCTTCAAACCTTTTGCTGAGGGTCTGTGACCACTGGAATGAACCGAATGGTTTGGGTTAGGATGTGGAGTGTGGTGAAACGGTGCATGGGGGGACCTTGTGCTCATCTCAGGGCTGGCAACTGATGCTCCTTCCCTCGCCCTTCAG
Seq C2 exon
ACTCAAAAGGTCTCTCCAACCCGGCTGAAGTGGAGGCATTACGGGAGAAGGTGTACGCATCGCTGGAGGCGTATTGCAAGCACAAATACCCCGACCAGCCCGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002626:ENSGALT00000004139:8
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(16.3=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(18.4=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:
AGTACTGACAGAACTCGTGTCGA
R:
CTGGTCGGGGTATTTGTGCTT
Band lengths:
190-1049
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]