GgaINT1024254 @ galGal4
Intron Retention
Gene
ENSGALG00000002626 | RXRA
Description
retinoid X receptor, alpha [Source:HGNC Symbol;Acc:HGNC:10477]
Coordinates
chr17:7329258-7330179:+
Coord C1 exon
chr17:7329258-7329279
Coord A exon
chr17:7329280-7329907
Coord C2 exon
chr17:7329908-7330179
Length
628 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TTTTGTCTTTTTTTTCTCTCTTC
3' ss Score
-6.56
Exon sequences
Seq C1 exon
TCAGACACCAAGCATTTCCCAG
Seq A exon
GTAAAGGGACATATAGGTTTGAGCAGTACCTGGCAAAGTAATGACAGTAATGGTAAGGATTCATATGTTTCCAAAGGAGATACAGAGGGACTTGGCAGATTTTAACAAAGTGAAGAAATTATTCTCAGGAGAAATGCTAAAAGATAAGAGTGCCCTTACCCCCCCCCCCCCAGTGCTGCCTGCAGCGATCAGTGTGCCCTCTGCACAGCTCAGCTTGCACAGCCCCCCGACCCTGCTCCTCATGCATGGTCTGGCCCTCTGCACCTTCGCTTTAGCATCCCCTTTAAATCTGAATTGTGGCGTCTGTAGGGTGGGCCCTGGTCCTGCATCCCCTGGTCCTGCATCCCATAGTTCTATACCCTGTGGTTCTGCACCCTTTGGGGAGCAGTGCTGCTGGGTACAGGGGGTGAAGGAGGGAGGAGGGCAGTTGACAGCTCTGGAGTTGGAAAACTGTCTGCATTGGTGATTTTTGGGTCCTACACCAAAAGGACCCAAAACAAAAGGGGATTTCGGAAGCAGTGCTGATGGAGGAGAATGCATCAGGAGGTTGGGGGTGTTGAAAAGCAGCCTCTGAAGGTCTGGCTGCCATACCAGATGAGACTCAACCCTTTTGTCTTTTTTTTCTCTC
Seq C2 exon
TTCCAGATTTCTCAAACCAAGTCAATTCCACATCCCTGAACTCCCCGACGAGCCGAGGCCCCATGGCCACCCCATCCCTGCACCCGTCCATCGGGCCGGGCATCGGCTCCTCGCTGGGCTCCCCGGGCCAGCTGCACTCACCCATCAGCACCCTGAGCTCACCCATCAATGGCATGGGGCCACCCTTCTCCGTCATCAGCTCCCCCATGGGCCCACACTCGATGTCTGTCCCCTCCACGCCCAGCCTGGGATTCGGCACCAGCAGCCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002626:ENSGALT00000004139:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.945
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF118253=Nuc_recep-AF1=PU(69.8=89.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGACACCAAGCATTTCCCA
R:
CTGCTGGTGCCGAATCCC
Band lengths:
287-915
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]