BtaINT0127968 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000602 | RXRB
Description
Bos taurus retinoid X receptor, beta (RXRB), mRNA. [Source:RefSeq mRNA;Acc:NM_001083640]
Coordinates
chr23:7325636-7326944:-
Coord C1 exon
chr23:7326534-7326944
Coord A exon
chr23:7325884-7326533
Coord C2 exon
chr23:7325636-7325883
Length
650 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TACCCTCCCTCGCCCCCCAGACT
3' ss Score
10.35
Exon sequences
Seq C1 exon
CCAAGATGGCTGCCACATTGGCGCTGTCATTTTGGTACAGGGCCGGGCGAAGCGCTTAGTTTGACCTGGTTGAAGCCAGAGTCGTTTTCTCTGGGGCTTCCTCGTGCTCGGCTCGTCCCCCCGAGCGGTCCTCGGGAATCCCTGGTGCCGCTCGGCGTCCTTACACTCTGCCGGGAGTCATGTCTTGGGCTGCGCGCCCGCCCTTCCTCCCCCAGCGGCATGCCGCAGGGCAGTGTGGGCCGGTGGGGGTGCGAAAAGAAATGCATTGTGGGGTCGCGTCCCGGTGGCGGCGGCGGCGGCCCTGGCTGGATCCCGCGGCGGCGGCGGCGGCGGCGGCGGCCGGAGGACAGCAGGCCCCGGAGCCGGAGCCGGGGGAGGCTGGACGGGACGGGATGGGCGACAGCGGGCGGG
Seq A exon
GTGAGTGAGCCCGCAGACGGGCCCGGGCGCCGAGACCCCGACGCCGGCGGCCCCTTCCCCCTCCCGGGCGCTCTCCCGGGCGCCCCCGCCCCCTTGTTTGTAAACACGCGTCCCCTCCTCCCGGGGGCCGCAGTGCCCTGCCCCCGGGGCGGGGCGGCCAGGGGGCGCTTCCGCTCTCCCAGTGGCGGCCGCCGGAGGCCCGGCTCCCCCGCGGTCCCCGGCGCAGGGCCCCAGTCCTCGAGCCTGAGGACCCTGGACGTTGGGAGGCGAGTTCCGCGCCCTCGGCGGGGTCTCTCCCCTGCACGTTCGGGCGGCGAGCTGGGAGTGCAGAGGCTGGCGGGTTCCCCCCACGTGCTGCCCCACCCACACGAGACGCGTCCGGCCTGGGGTGGCCAAATTCACTACTTGGAGCTTGCCTCTCGTCAGCTCTCCTCTCGTTTGTCAGCCCCCTCCTCCCACCACGATTAGGGGTTCAGCCCTTGTTTGGCAGTAGGCTGTCTGGACTTGGGAAGGGGTGAGATGGGGGCGCGGTGGGGAAATCAGAGAGAGAGAATGAAGTCTCCCGTTGGGTGATCCAAGACTCATTTTCTCTTTTTGTCTCTCCTGTCTCTGTGTGTCTGTGCCTGTGTGTACCCTCCCTCGCCCCCCAG
Seq C2 exon
ACTCCCGGAGCCCAGACAGTTCCTCCCCAAATCCCCTTCCCCAGGGGGCCGCTCCCCCTTCTCCTCCAGGACCACCCTTGCCCCCTTCAGCAGCTGCGTCCCTTGGAGGTTCTGGGGCTCCACCACCACCCTCGATGCCACCCCCACCACTGGGCTCCCCCTTCCCAGTTATCAGCTCTTCCATGGGGTCCCCCGGCCTGCCCCCTCCAGCTCCCCCAGGATTCTCCGGGCCTGTCAGCAGTCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000602:ENSBTAT00000000860:1
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=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF118253=Nuc_recep-AF1=PU(65.8=90.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGGGGGTGCGAAAAGAAAT
R:
TGATAACTGGGAAGGGGGAGC
Band lengths:
344-994
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]