BtaINT0127967 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017851 | RXRA
Description
retinoid X receptor, alpha [Source:HGNC Symbol;Acc:HGNC:10477]
Coordinates
chr11:106012705-106015000:+
Coord C1 exon
chr11:106012705-106012810
Coord A exon
chr11:106012811-106014738
Coord C2 exon
chr11:106014739-106015000
Length
1928 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGC
5' ss Score
7.93
3' ss Seq
TCACGCGGCTTCATCCGCAGGTT
3' ss Score
10.03
Exon sequences
Seq C1 exon
ACTCCAAGGGGCTCTCAAACCCAGCCGAGGTGGAGGCGCTTCGTGAGAAGGTCTATGCGTCCCTGGAGGCGTACTGCAAACACAAGTACCCCGAGCAGCCAGGAAG
Seq A exon
GTGGGCCTTGGGGGCTGCGGCAGGCCCGCCCCAGCCCTTCAGACACTCCTGTGGGTTAGAGGGCAGCTGCCCTCCCCCACCCAGGGCAGCGGGGGACCCAGGCACTCTTCCGCCCCAGCAGGCGTGCACTCACCGTTCCCTGTAGCCCCACCAGACAGATGGGCCCTGTGCTGGCACACAGTAGGCACGCGTGGCTCTAGAGCGGGTAAACCAAGGCGGTGCTTTCCTCTGCCGGCCAGAGGAAACCACTCGAGGCAGGGCTCTGCTGTGCTCGCCCCGGCAGGGACGAAAGCCAGCACATAGTAGGTGCTTTACAAACGTGTGTGGAACAGATGGCTGTGATCTGAGCGCAGTCTGCCTGGCTCTCTCCCTGCTGACTGTGGGCCTGGGAGGGCTGGCCTTGCCTCCTTGCCGGGTCCCCCGAGCCGGGCGCGCAGTGGGTTTCTGGGAGAAGGTGCCTGCAGACCAGCTGTCCAGGTTCCTGCCTCCTCTCTTCCTGGACCGGCCTCTGTCTGCCCGGAGCGGGTGGGGCCCCAGGGCCCCAGGCCTGGCTCTGCCCTCGCCCGCCCCGCCAGCCGGCACACACACGGTTAAGTGTCTGACCAGCCTCATCTGGTTTAAAGTGAAACTTCCCGGAGGAGGGGTGGCAGGCCCGCCTGTTTTTCCTGGCTCCTGGCCCTGGCCCATCTCGCCAGCTCAGCAGAAAACAGCGCGTTCTTTGGCCCCGCTCCAGCCTCTGAGCTGCGTTTTTGCCTTTAAAATGTGGGTTGTGCTGCAGCCAAGCCCGGGGCTTTCCCCCTGAAATAAGACATTGTTAATAATTAGTGAGGTCCCAGGGTCCCCCGAGGGTCGTGTGGAGAAGGCCTGGAAGCACCCGGGGTGGGGACTGGGGTCCGGGGAGGGGTGGATGTGAATGTCCGGGTGGGGCATTGGGCCCTGTCCCCACACGGCAGCTGTCCTTGGCACAGAGTGCAGGAGCCTGGCGTCCCTGATCCAGGCGCCCCCCCCCCCCCACCAAAGTCTCCCCTGCTCCTCCGCTGCCCAGTGTCCTTCCCAGAGACTCTGCAGTGGGGCAGGCGCAGCCCGAGGAGCCCCTCCCCCTCCCTGCACCCGCCCTGTTCGAGGTCGGGCTGCTGTGCTGCAGCTCTTTCCGGGCGAGGTGGGTGCTGGCGTGAGCCCCCCTGGAGGCCTCTTGGAGTTCAGACTTGCCCCCCAGCTCAGGAGCAACTTCATCCCGAGAGGGGGTTGCCCGGCGGCCAGGGGCTTTGCTGGTGCTCAGATCTGCCGTCAGAGCCCTTCTTCCCGCGTAAAATCCTGCTGCGACTCCTGCTGCCCTTGGAGAAAGCCTGCCGCGCCTTTTAACGTCCCCCTCGAAGCCCTGATCACCCCGCCCCTGCCCGGCCACTGGCCCTTTATCCTGAATCTCTGCCCTGGGGGTGTCCTCTTGGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAGAGACCCCTCCCCGTTCAAGGGCCCCGGCTCAGGCAGGTCCCCTGCCGTGGCAGCCTCGGGGGCTGGGGCGGTGAGACGGTCAGGCCACGGGGCCCGGGTGGGGGAGCGCGGCGGGCGCTCACGCGGCTTCATCCGCAG
Seq C2 exon
GTTCGCCAAGCTGCTGCTGCGCCTGCCCGCTCTGCGCTCCATTGGCCTCAAGTGCCTGGAGCACCTCTTCTTCTTCAAGCTCATCGGGGACACGCCCATCGACACCTTCCTCATGGAGATGCTGGAGGCCCCGCACCAGATGACTTAGGCCCGCGGTTCCCGGCCCGCCCCGCCCTCTGCCCGCGGGCCCTGGGGGCGTGGCCCGCCTGGCCCTGGGGGCGTGGCCCGCCGCTGCTGAGCCTGTGCTGCAGGCCGCCCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017851:ENSBTAT00000023729:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(18.7=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(15.0=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:
ACTCCAAGGGGCTCTCAAACC
R:
AACCGCGGGCCTAAGTCATC
Band lengths:
264-2192
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development