BtaINT0127960 @ bosTau6
Intron Retention
Gene
ENSBTAG00000017851 | RXRA
Description
retinoid X receptor, alpha [Source:HGNC Symbol;Acc:HGNC:10477]
Coordinates
chr11:105990344-105996858:+
Coord C1 exon
chr11:105990344-105990658
Coord A exon
chr11:105990659-105996707
Coord C2 exon
chr11:105996708-105996858
Length
6049 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
ACCCCGCTTTCCCTCCGCAGCTC
3' ss Score
12.15
Exon sequences
Seq C1 exon
TCGCCGGTGTGGGCTCCTGACCAGCCTCCTGTGGCTTCTTGTCTTGCAGACTTCTCCACGCAGGTGAACTCCTCCTCCCTCAGCTCCCCCACGGCGCGCAGCTCCATGGCCGCCCCCTCGCTGCACCCCTCCCTGGGGCCCAGCATCGGCTCCTCGCTCGGCTCTCCGGGACAGCTGCACTCACCCATCAGCACCCTCAGCTCGCCCATCAACGGCATGGGCCCGCCCTTCTCGGTCATCAGTTCCCCCATGGGCCCGCACTCTATGTCGGTGCCCACCACACCCACCCTGGGCTTTGGCACCGGCAGCCCCCAG
Seq A exon
GTAAGTGCGGGGAGGAGCCTGGGCCAGGGGCAGGGCCTGGACTAAGGGGCGGGGCCAGTGCCAGGGGGCGGGGCCTGACTTTACCTGCACCTTCTATGTTGGCTCAGATAGTAAAACGTCTGTCTACAATGCAGGAGACCTGGGTTCGATCCCTGGGTCGGGAAGATTCCCTGGAGAAGGAAATGGCAACCCACTCCAGTACTCTTGCCTGGAAAATCCCATGGATGGAGGAGCCTAGTGCAGGCTGCTGTCCGTGGGGTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGGAAGGTCCCAGTAGAGAAAGGCCAACCCCACAGGGGGAGGCCCCCCATAAAGGAAGGCACCCCCACCCCAGTAGAGGAGGCCCCCATAGAGGGAGGATCCCCATAGAGAGAGGCCTCCCATAGAGAAAGCACTGCCCCCATAGAGGGAGGTCCCTGTAGAGGAGGGCCCACCAGTAGAGGAAGGCACCCCCACCCCAGTAGAGGAGGCCCCCATAGAGGAAAGCCCCTCCCATAGAGGAGGCCCCAGTAGAGGAGGCCCCCATAGAGGAGGCCCCCGTAGAGGAAGGCCTGTCCATCAAGGAGGCCCCAGTAGAGGAGGGCCCTATGACAGGAGCTCTGGGAGCTGTCTCCCTGAGGGGGGCAGGACAGCCGTCTCAAGAGGGACTCCAGCACAGGCCCCCCTGCCCAGAGACGTGTGGCTAACGGTGTCAGCGTGTCCCGCGGGCTCCCTGCTGCCCGGGAGCAGCTGCCTCCAGGACTCTCCACTCCTGGGATGCCTTGAGGTCTGGAGCCTGCCCCCTGCCTGTCAGCTAGGCCTGTCCGGAGCTGGTCTCGGTGGAGCCCCCCTCTGGCTCTCCAGGCCCCTCATCAGCCCCTTTGTTCCTGGGGAGCCCATGCTCCCTTGTGTCCGGGCCTTCCAGAAGCAGACAGAAGGCTGGAGGGTTGGTGCGAGGGGTCTCAGCTGCCTTCCTGGGCCTGACCGTGTTCTTTGTAGCGTAGCCACCACACCCCGATCCTCGCTGGCTGCAGAGTGCCTGCTGCTCAGCGAGAGGCAGACGAGGCCCGACCTGCACCTGTCCCCTGGGAACTGGGCCAGAGGCAGCACCTGCTGGCTCTCAGGCCTGCGAAGCTCCTTGCTGCCCTCTGGCCTGGTACCTGCCCTGCACGCCTCCAGGGCTCATGTGCGGAGGAGCCTGGGTGCGAGTCTGGAGTGGGGGCTCTGCGGGGTAGGGCCCGAGGGTGTCAGTGATGCCCCCAAGCTTTGGGGTTAGCCTTTCTGGGGGGGCGGTGCTGGGGGGTGCAGTGGTGCCCCCAGGCCTTGGGGTTAGCCTGTCTGGGGGGGCGGTGCTGGGGGTGGGGGTTCGGGGCCTCGTCTGTCCCAGTCTGTTGCCGCCGGCACGCGATGGGTGCTTGTTGAGTGCAGGTGCTTGTGAGCGAGGAGCCGCAGGTCCCGAGCCTGATGCCGGGGCTCAGGGAGTGGAGGGGGTGGGTGTGTCCCCGGACGTTCGCTGCGACCCACCGCTCAGCTGTCCGCCTGTCCTTCTGTAGGTCAGTCGGGCCGCAGGGGGCTTAGCCGCGGTCCGAGCCCTGGGATCAGCCTCTGGCCACCATTCCTGGGAAGGCCTTAGTCCCCACCACCCTGCCCCCCATAACTCCTTCCCTGGGAGCCGAGTTCAGCTTCTAAGCTTCAGCAGTTTGTCTTAAAAACTTGGGGTTCCCCATATTCATGGAAGTGTGGGTGGAGTTCGGGGGGGCATCCCCCCACCTCCGACTCAAAACCACAACCGCGGAGTCATGGGGCCGGAACCAGTGAGGCAGTCTGACTCCTGCTGCTGGCGGGGATGGCCCCCGACTCGACCGCGCCCTGCAGGGAAGTGGATGCGGGCGGTGCTGGGGGCTCTGGGCAGAAATGGGCCGGGCCGCAGGCACCGTGGGCTGAGCTGCCCCTCCTCTCCCCTGGTTCAGGGGCTCCATCAGCCCAGGGGGCGTTCCCCACCTCGGCCCAGAGCTCGCCTGCAGTGCTAGGCACGTGTGGGCACCTTGGCGCCCTGGCCTCACCACCCTGATCAGCCTCCCTGGGCAGGACCCGCATGGGCCCTGCCTGTCCTTGCTGTGGGCACCACGGCCATGAAGCTGCGTCCACCAGGCCATGTGTAGGGGTTTGCCCCCAGCCTTGATGGGCAGGCAGAGGCCGGTGGGGTCCAGGGGCCTCCCACCCCATGCTGACGGGGGTGATCGGCTTCACCTGCGAGGGCTGGAAAGGAAGGGTGTGGTGGGCGTGGACGAGGGGCGGCGAGAGACAGGAGATCACTGAAGGCTCCGCGGGAACTGAGGTGAATGCCAAGGATGTGAAAGGGGAAATGGGATGGGCCCCCACCCTGGGCACACCACGGAGCCGCCACTGATGCTGACCATACCTGAGGGCTCCGTCCCTGGTGCTAAGGCCCGCCTCAGGTTATGGAGGGCGGACACCGGTCCCGAGGGCCTGCCTGTGGTGGCCTGGGGGACAGGACAGGTGGCCCCTACTCACCCAGCATGGTTTGGACAGCCACAGAGGAAGTGCCCGAGTTCCTTTCCGGGGTGCTGCCCAGCGGATCCAGCTGTTCAGTGTTGCAGCCGGGCTCCCACAGCCCGCGGGAGGCCTCGGGCCCAGCCTCTGGCCCACACAGTGTCCTCAGGGCCCCTAGGGCCCTCCCTTGGCCTCTGCTGCTGACTGGCCACCCCGGCCACCCCAGTCTCCTGCCCTTTTCCCAGCAGTCCTTTGGTGTGCCCTTCTCCAAGCATGTGCTTGGCGGCCCCCTCTGGCTGGGAGCTGCCTTCCGTCCTCTGCGGCCCAGCCGGCCTGGGGCTGGCCCCCGGAGGCCCCAGTAGTCCTGCAGAGGCTGCTTGCTGTGCCCTGAGCTGGGTTCAGGAGCTCTGCTGTCAGCGCGGCCCCCAGATTGCTCTGTCATCCCAACGGCGACTTTCGGACGGAGACACTCCTGTTTATCCGGTTTTTACACAAGAAGCCTCAGGCCCAGGGCGGTTAGATAATTCCCCCAAAGTCATTCAGGGAACGGAGGAGGCAGAACCCTCATGGTCAGCTGTGGCCGAACCCCCACCTCCTGGCGAGCCCCACGGGCTGGGCAGGGGGTGTTCTCCGTGGCCTTGGGTGCCTGGCCGGGTGCTCGGTGGATGGTCTCGCGGCTCTGGGCTGGCCTGGGGCCCTGGACACCCTTTCTGCAGCATGCAGGGAGTCCCTCAGACTCCCAGAGGCCCGAGCTCACACCTGCGTCACCCCTTAAAGCCGTGTGCCCCTGGCTGGCCGCTGCATCCACTCTGGAGGTGGGTGGGCGGCTCTCCCCGCTCACTCAGGGCTTCCCATGGGGTGCAGCCCGATGGCACTCGGCAAATAGCCGAGGCCCCCGCTGAGTTGACCGTCTTCTGGGAGATGCTCCTGAAGCCTGCAGACTGTGCTGGGGGGTGGGGGGTATTCTTGGAGGCAGTGGGGTTCTCTGGACACCCCTCACCCCTCCCCTTGGGTCCTGACAGCCCCACATGGCCGGAGCTGGCCTCCCGGCCTCCCTGCAGCCCCCTGAGTCCCATGGGCTTCAGCGTCCTCAAGGAACCAGGTGGCCACCTGGGCAGGCGAGCCCAGACGTCCAGGGCTGGAAGAGCCCCTGCAGGTGCTCAGCGAGTGCTCTGTGCACGCTGAGCACCAGCTCCTCCTGTCCTGGGAGGAGGGGGATGGGAATCGGGGCCCACAGGGAGGGAAGGGGGTGAGGCTCCCATGTGCAGGAGGAGCCCAGCCCGGGGAGACCCGGGGGCAGCGCGGCGGCTGCGGTCCGTCCAGAAGAGCTGCAGGACCTGACTTCCGCCTTGGTCAGGGCTTTGCAGAAGTGAGGGTGCTGGGGGGCTGCCGGCTGGCGCCCTGGCGCCTGTGGGGTGCGGCTGGCTTGCAGGGTGTGGTGGGAAGCACCCCTGGGCCCTGGGCGCTGAGGGGAGAGCTGGGGTGGGCGCAGCGGAACCAAAACTGCTGTGTCACTGCCGCGGCAGCTGTTGCCACGGTGACCGGTGAGTTTCCCACGCTTCCTCCTGGCGCAGCGTCAGGATGGCGGGAGGGGCGGAGGGGGTGTGTGTGTGGGTGAGGATGTGTGTGTGTGTGTGTGTGTGTGTGTAAGGATTGTGTGTGTGTGTGTGCGTGATGGCGGGAGGGGCGGAGGGTGTGTGTGTGTGTGAGGTGTGTGAGGATATGTGTGTGTGTGAGGATTGTGTGTGTGTGTGTGATGGAGGATGTGTGTGTGTGAGAGGTGTGTTTGTGAGGATATGTGTGTGTGTGTGTGTGTGAGGATTGTGTGTGTGTGTGTGTGAGGATTGTGTGTGTGTGTGTGAGGATTGTGTGTGTGTGTGTGTGAGAGGTGTGTGTGTGAGGATATGTGTGTGTGTGAGGATATGTGTGTATGTGTGAGGATATGTGTGTGTGTGTGAGGATTGTGTGTGTGTGTGTGTGATGGAGGATGTGTGTGTGTGAGAGGTGTGTGTGTGAGGATATGTGTGTGTGTGTGAGGATTGTGTGTGTGTGTGTGTGTGATGGAGGATGTGTGTGTGTGAGAGGTGTGTGTGTGATGTGTGTGTTTGTGTGAGGTGTGTGTGAGGGTTGTGTGTGTGTGTGTGTGTGTGATGGCGGAGGATGTGTGTGTGAGGTGTGTGTGTGAGGATATGTGTATGTGTGAGGATTGTGTGTGTGTGTGATGGAGGATGTGTGTGTGTGAGAGGTGTGTGTGAAAGGTGTGTGTGTGAGGTGTGTGTGAGGTGTGTGTGTGTGAGGATTGTGTGTGTGTGTGTGTGTGATGGCAGAGAATGTGTGTGTGAGGTGTGTGTGTGAGGATACGTGTATGTGTGAGGATTGTGTGTGTGTGTGTGTGTGTGATGGAGGATGTGTGTGTGAGGTGTGTGTGAAAGGTGTGTGTGTGAGGTATGTGTGAGGTGTGTGTGTGAGGATTGTGTGTGTGTGTGTGTGTGATGGCGGAGGATGTATGTGTGAGGTGTGTGTGTGAGGATTGTGTGTGTGTGTGTGTGTGATGGAGGATGTGTGTGTGTGAGAGGTGTGTGTGTGAGGTGTGTGTGTGTGAGATGGCAGAGGATGTGTTTGCGAGGATTGTGTGTGTGATGGTGGAGGTTGTGTATGTGTGTGTGAGGTGAGTGTGTGAGGATTGTGTGTGTGTGTGAGATGGCGGAGGATGTGTGTGAGGATGTGTGATGGCGGAGGATGTGTGTGTGTGTAGGGGTGCTGTTTCCTCCCTCTCTACTCGGGTTGCAGGATCTGAGACCGCCACCATGCCGTGTGTGTGTGTGTGTGTGTGTGTCCGTGTGTGTGTGTTTGAGGATTGTGTGTGTGTGTGTGAGAATGTGTGTGTGTATGTTAGAATGTGTGTGTGTGTGTGTGTGAGGTTTGTGTGTGTCTGTGTGTGTATTTGGTGTGTCTGTGTGTGTGTGAGGGTGTGTGTCTGTGTGTGTGTGTAGGGGTCCTGTCTCCTCCCTCTCCCCTCCCTCCTCTCTGGGGTCAGGCTTCGGTGCCCATCCATGGGTTGGGGTCCCTAAAGCGCCCGCCACAACAGCGGGTCCCAGAGCTCTGGCTGACCGCTGGGGGCAGCACCCGGGGGTGGCAGGCAGTTCTCACTTTGGCCGACGAGGGGCAGGGGTGGGAGCCGGGTCCTCCGAGCCTGGGGTTCCTTCGAGCCTGGGGTTCCTTGGGAGCTGGGGCTCTGGGGGCAGGACGGCCTCCTCCAGCCTGGCCAGGCCGACGGGGTGGACATCCTGCCGGGCTCCGTGGGGCTGGGCCTGCCGGGCCACAGGGCTGGGGGTGGGCGAGGCCCCCTCCGAGCCCCGGTTTCTCTCTCCGTGGAGGGGGGCGTGGCAGCGCCTTCTTTGCCCCGCGGATGCCCCGCAGCGCCTGCCAGGGCCGACCCCGCTTTCCCTCCGCAG
Seq C2 exon
CTCAGCTCGCCCATGAACCCCGTGAGCAGCAGCGAGGACATCAAGCCCCCACTGGGCCTCAATGGTGTCCTCAAAGTGCCGGCCCACCCCTCAGGGAACATGGCGTCCTTCACCAAGCACATCTGTGCCATCTGCGGGGACCGCTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017851:ENSBTAT00000023729:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.819 A=NA C2=0.490
Domain overlap (PFAM):
C1:
PF118253=Nuc_recep-AF1=PU(69.8=77.1)
A:
NA
C2:
PF118253=Nuc_recep-AF1=PD(28.4=64.7),PF0010513=zf-C4=PU(15.7=21.6)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development