BtaINT0127964 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017851 | RXRA
Description
retinoid X receptor, alpha [Source:HGNC Symbol;Acc:HGNC:10477]
Coordinates
chr11:106007652-106009161:+
Coord C1 exon
chr11:106007652-106007781
Coord A exon
chr11:106007782-106009028
Coord C2 exon
chr11:106009029-106009161
Length
1247 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CCTGTGCCCCGCCCCCGCAGGCT
3' ss Score
11.49
Exon sequences
Seq C1 exon
CCCAACGACCCCGTCACCAACATCTGCCAAGCGGCTGACAAGCAGCTCTTCACACTGGTGGAGTGGGCCAAGCGGATCCCGCACTTCTCCGAGCTGCCCCTGGACGACCAGGTCATCCTGCTGCGAGCAG
Seq A exon
GTGAGCGGCGGGCCGGGTGGGGGCGGGGCGAGGGGTGGGCAGGGGCGGTGGGCGGGGCCTGAGGGGGCGGGCCTTGTGAGGGGGCGGGGCCCTGCTCATGCTCAGTGGGGTCCTAGAGGCATGGGGCACGGGGCATAGGGAGGGGGGTGGGGGGCTCTGCTGGGGAAGGGCCGGGGGGCGGCTGGGGACGGGGCCTCAGAGGAGGGCAGTCTTGCTGGGGGCCCGGTTCTGCCCCTTGATGAGGTCTCCTCCTCAGCCTCCTGAGCCCTGGTGTCTGGCCGGCGGGTGTCGGTCCACGATGGCCCAGGGGTGGGGGAGACGGTCCCTGGAAGAGCTTTCACTCTGACTGGGGCACAAACTCCAACCCCAGAGCCGACAGGAAAAGATGCCGACCTGCGGGGTGGGGCGGGGCCCTGGGTCCTCATGCTGAGCGGGCAGCCCCTTTGTCTCCCGGGCTCTCAGTTTTCCTCTGTGTTAAGTGAGGCCAATACTAGCTTCGTGGGGTTGAGTCATGATTGAACAGGATCACCGTTGTGACACGGTCACAGCCACCAGCCCGGAGCCTTTGGGGCACCGGTGACGGTCACAGCCACCACTGCCGAGTGCTCCGTGGGCTCCGGGCTGGGGTCTGAGACGGTCGCTAGCGATGCTCCGGAGATGGCTCGCGCGGCCGGTTTGCAGGAGCGCATGCGCACGGGGTCTTTTCTCTGCCCTCCCCCAGCCCTGCGCCCACGCCGCGTGTGCCAGGGACTCTCAGAGAGAGAGTGGCAGTCCCCCTTTGGCTCCAACACTCCTGGGTTCCATCATTTACTGTTTTGTGGCACCCCCAAAACGTCAGCTCTGGGAGTCTGCGTTGGGGGCTGCCCAAGAGGGTCTGGGGGCTCCCTCACACTCTTCGGCAGCAGCGGCGTACAGAGAGGGACTTCCCGGGCATCTGAGTATGGAGGGCCCGGGTGAAGCAGCTGCAGGAGCTGCTCTGTGCGGGACTTTAGGGTCAGTGCTCGGGAACCGCCCTTCTGTGGCAGGGTCATGGGCTCGGGGTTCCATGGAGGCCCTCCCTCGAGAGGGTGCGAGCTGCCTCCGGGGGGCCCGGTGGGGGCCGGGGCGGGGCGGGGTGGGGTGGGGCAGGGCCCCGGAGCCCTGCAGGTGGACGAGTCCCTGCTCCTGCTCAGTGTGGGGGTGGTCCTAGGGGCGAGGAGGCGGGCGGGGCCTGGAGACCACGGTGACCCTGTGCCCCGCCCCCGCAG
Seq C2 exon
GCTGGAACGAGCTGCTCATCGCCTCCTTCTCGCACCGCTCCATCGCCGTGAAGGACGGCATCCTCCTGGCCACCGGGCTGCACGTACATCGCAACAGCGCCCACAGCGCAGGCGTGGGCGCCATTTTCGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017851:ENSBTAT00000023729:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(23.0=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(23.5=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:
GACCCCGTCACCAACATCTG
R:
CTGTCGAAAATGGCGCCCA
Band lengths:
257-1504
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development