GgaINT1024260 @ galGal4
Intron Retention
Gene
ENSGALG00000002626 | RXRA
Description
retinoid X receptor, alpha [Source:HGNC Symbol;Acc:HGNC:10477]
Coordinates
chr17:7348013-7349643:+
Coord C1 exon
chr17:7348013-7348145
Coord A exon
chr17:7348146-7349551
Coord C2 exon
chr17:7349552-7349643
Length
1406 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
GCTTCTCGTGTCCTTTGCAGAGT
3' ss Score
10.12
Exon sequences
Seq C1 exon
GGTGGAATGAGCTCCTCATCGCCTCCTTCTCCCACCGCTCCATAGCTGTGAAGGATGGGATCCTGCTGGCCACGGGGCTGCACGTGCACCGCAACAGCGCGCACAGCGCCGGTGTCGGGGCCATCTTTGACAG
Seq A exon
GTGGGAGAATGGAGTGGGTGGGCGGCATGAAGGGAGCTCCAGGCTCTGTCCCTGTGCTCCGTGTCCCCCATTGGAACATCTCCTATGTGCATCCTCTGGGCACATCATGTCGCTGCTCCTCGGTGTGCAGAGCCCAGCAGGACAAAATAGCCACAGAGATCACTGCCCATTGCAGAGCGATGCTTCTGCCGTGGGGTCCAGATGCCTCCCAGTGTTGGGAGGGGGCTGCTGCTTCCTTTCCATTTCTAATTGGGCCGAGACGTGGTTTTGTTGTCGCAATGAAAAAGCACCAGAAATACCCAGTGGGTTCCACAGGGACATCCCGGTGGCTCTTCAGTCATTGTGCTTTGGGGAAATGCTTTAGGGCAATGCATGCAGATTGTTTGCCCCCCAGCATGGCTGTGGGCATCGCTCACACTGTGGCTGATTTGAAGAAAGGTTGAGGGAACTGAGCTTGTTTAGCTTAGAGAAGAGAAGGCTCCGGGGAGACCTCACTGTGGCCTTCCAGTACTTGAAGGGAGCGTATAAACAGGAGGGGGAATGGCTGTTTACGAGGGTGGATAGTGATTGGACAAGGGGGGATGGTTTTCAACTGAGACAGGGGAGGTTTAGGTTGGGTATGAGGAGGAAGTTTTTCACACAGAGGGTGGTGATGCACTGAACAGGTTGCCCAAGGAGGCTGTGGATGCCCCATCCCTGCAGGCATTCAAGGCCAGGCTGGATGTGGCTCTGGGCAGCCTGGTCTGCTGGTTGGTGACCCTGCACATAGCAGGGGGTTGGAACTGGATGAGCGCTGTGGTCCTTTTCAACCCAGGCCATTCTGTGATTCTATGATATGATTCTGATTTCTCTGCCCCAGCCTCATCCTGAGGCACTGACTTGGAACCAAACCAGGGGTGCTTTCTCAGTTTGCGAGGAAATTGCTCTTCAGTGCTGGGTGACATCATCTGTTTCCTGTGAGGTCATAAGTGCAAGCTCATGACTTCACTGCAGGCTCCAACAGGAAATTCTGGGCAATCACTGGAAAATATTTCAAGACCGGCACCTGCAGAAGGAGCAAAGGGAGCAGTAAAAATTACCAGCAGAGGAAATTGCTTTTAGATACCTGCCTTTTTTTTATTATTATTGTTACTGTTTTTTATTTTCAGGCAGCTTTCTCAGGTGCCAAATCCACAGTGAATGCACAGAGCCAGTCCTGCTGATCTCTGTTCTGTCTCACAGGAACTGCTGATGTTCCTGACGGGCGATTTTTGGTACAGGAGGAAAATGAGGGCACATCCTGGTATAGACGAGCCCTATCCCATGACTTTATTTAACATGCGCCTCTCTCTGGCTCTGACACCTGTTTTGCTTTATTTCCTGTTTCTTGTTCATGCTGACGCCTGTGCTTCTCGTGTCCTTTGCAG
Seq C2 exon
AGTACTGACAGAACTCGTGTCGAAGATGCGAGACATGCAGATGGACAAGACAGAGCTGGGCTGCCTGCGAGCCATCGTCCTCTTCAACCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002626:ENSGALT00000004139:7
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(23.2=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(16.3=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:
GAGCTCCTCATCGCCTCCTTC
R:
GGTTGAAGAGGACGATGGCTC
Band lengths:
214-1620
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]