BtaINT0127966 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017851 | RXRA
Description
retinoid X receptor, alpha [Source:HGNC Symbol;Acc:HGNC:10477]
Coordinates
chr11:106011163-106012810:+
Coord C1 exon
chr11:106011163-106011254
Coord A exon
chr11:106011255-106012704
Coord C2 exon
chr11:106012705-106012810
Length
1450 bp
Sequences
Splice sites
5' ss Seq
CCGGTACTG
5' ss Score
5.61
3' ss Seq
TGGCCCCTTCTCCCCTGCAGACT
3' ss Score
10.67
Exon sequences
Seq C1 exon
GGTGCTGACGGAGCTGGTGTCCAAGATGCGGGACATGCAGATGGACAAGACGGAGCTGGGCTGCCTGCGCGCCATCGTCCTCTTCAACCCCG
Seq A exon
GTACTGCCTGCCATCCAGGCCTGGTGTCCGCCCCGCCAGGGGCCAAGGCCGCGGGGCGCCCACCGCAGCCCCACAGCCCACTGATAGGGCGGTGTCGGCCCCCTGCCCCTCCTCTGAGCCTGCCTGTCTCCCTTGCGATGGGCTCTGCTGCCAGAGATTTGGAGCCCGGCTGCTCTGGGGGTGCTGGGGGGTACTGGGGCAGGGGTGGGCTCTGAGGGCTTCTTGGGGAAGTGCTGGCGGTGGGAGGGTGGGGCAGCGGCAGGGCTCATGAGTCCTTACCCTCCGTCGGCTCCAGTGCTGAGGGTCAGGCTGGGGTGAAGATGGGGTCCCCTAGTGGGTACAGCCCGTTTCCAGGGGCATTTGTCCCCAGGCCTGTGCGTGAGCCCACGACCCTGGCAACACAGCCCTGCCCAGCAGGGTCCCCCTTGAAGTCGAGCGTGACTTGGCTGCCAGCACTGCTTTACCTGCTGGGGCCCAGACTTGGGATTGCCAGGGGCAGAAGGGAGGTGGCCAGAGCTGGCACAGGCCCAGGTGTAGGGGGACCGGGGGCCCAGCTGCAGAGGAGTCTGCATTTCCCGAGGTGCCCAGGACCCCAGGCCACTGTGGCATTCACGCTGGGCACGGTGCCCCTGCTGGCATGTCAGACAGCCGGGGCAGGGCTGGTGTAGGGGCCCCTGGCCTAGGGCTCAGAGGCCACCCAAGAGCAGGCCTGTCCCCAGGGCTTCCCTGGCTTCAGATGGGCAGCAGGGGGGCTCCAGCCTCTGCCCCCTAAACCATCAGGGTGGACCATGCCTGTCTGGGGCCGCACTCAGGGCGGGGACCCGAATCCCAGTGCCCAAAGGGGGCTGCTGTTGGGGGTCAGTGGGGAGAGGCTTGGCGGGTGTCAGTTTGCGGGGTGACTTTGGAGACGAAGGAGCAGAGAGGGGCTTAGCTTTGCCCGACTGGGAGCTCTCACTGCCTCGGGGAGGCCTGTGACTGCTGCCCAGATGACCCAGGGCACCCGTGCGCCTCAGTCCTCAGCCCTGGGCCCTGGGGTTTTGGTGGCGCTGGTCCCAGGCATCTCTGTCCACAGGCAGAGCCCCTTCCAGACCAGGCTCCTGCTGCCAGGGTCCCAGGGCTCAGGGTGGCTTCAGCCCCCACAGCGTGGGTTTGGCTGTTTCAGACAGGAGGAGGTCTGGAGCCTACATTGGCTCAGAGGGGCTGAGACCCAGTGCACTGAGGCCTCTGGAGGTGACGCGGTTGCTGTGGTAACCAGGGGTGGGGGAAGCAGGCCTGTCCCACCCTCCTGATGAGGTAGTGGGGTGGCGAGAGGTTAGGGAATGGGCCCAAGGTCGAGTGGCCAGCATGCAGCAGGCAGGGTGCATGCACGGGGCCGCCTCATCCAGGCCGGGGCTCTGGGTCCCCGCTTCCCGGGGCCGGGCTCTGACCTGTGGCCCCTTCTCCCCTGCAG
Seq C2 exon
ACTCCAAGGGGCTCTCAAACCCAGCCGAGGTGGAGGCGCTTCGTGAGAAGGTCTATGCGTCCCTGGAGGCGTACTGCAAACACAAGTACCCCGAGCAGCCAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017851:ENSBTAT00000023729:7
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(16.6=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(18.7=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:
CTGACGGAGCTGGTGTCCAAG
R:
CTGGCTGCTCGGGGTACTT
Band lengths:
190-1640
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development