BtaINT0127969 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000602 | RXRB
Description
Bos taurus retinoid X receptor, beta (RXRB), mRNA. [Source:RefSeq mRNA;Acc:NM_001083640]
Coordinates
chr23:7324980-7325883:-
Coord C1 exon
chr23:7325636-7325883
Coord A exon
chr23:7325137-7325635
Coord C2 exon
chr23:7324980-7325136
Length
499 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCCTATTTCCCCCATCCCAGATT
3' ss Score
7.68
Exon sequences
Seq C1 exon
ACTCCCGGAGCCCAGACAGTTCCTCCCCAAATCCCCTTCCCCAGGGGGCCGCTCCCCCTTCTCCTCCAGGACCACCCTTGCCCCCTTCAGCAGCTGCGTCCCTTGGAGGTTCTGGGGCTCCACCACCACCCTCGATGCCACCCCCACCACTGGGCTCCCCCTTCCCAGTTATCAGCTCTTCCATGGGGTCCCCCGGCCTGCCCCCTCCAGCTCCCCCAGGATTCTCCGGGCCTGTCAGCAGTCCCCAG
Seq A exon
GTGAGAGGTCGTGACCACTTAACTGCCTCTCCACTTTCGTTTCCTTGTTTTCTTCCTGACCCTAGATCCTTGTATGAACTTCCCTGGTGCACTGAACTTCTAGTCTTGGCAGGCTTGTGGTCCTTGTGAAACCCCTGGCCCTTCCTGAGGTGCCACTGAGCTTTCAGTGCACGCCTCCTCGCCAGTGCTATAAAAGAACCTACTATTCTTGATGTCCGTTTTGTCTATCAGTGATTTTTTTGCCTTTTTGGTCCCATCTGCCCTTCTGAGATAAAAGCCCTTTGGGGCCGCTGTGTTGCACAGTTTCAGGGGACCGTTATGTCTTATCTCTTCGGGGTTGTGCTCCAGGGGTGGCCTTTCCCAGGCACGGCAGTGTAGTGTTCTTTGTAACGTGCGGTGCAGGGCCCTGCCTAGGTGGTAGAGAATGATGTCCGTCCCCTCTGAGAGATTATCCTTCCCAATGAGTCTCCCTGTGACTTCCCTATTTCCCCCATCCCAG
Seq C2 exon
ATTAACTCAACAGTGTCGCTCCCTGGGGGTGGGTCTGGCCCCCCTGAAGATGTGAAGCCACCAGTCTTAGGGGTCCGGGGCCTGCACTGTCCACCCCCTCCAGGTGGCCCTGGGGCTGGCAAACGGCTATGTGCAATCTGCGGGGACCGAAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000602:ENSBTAT00000000860:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.736
Domain overlap (PFAM):
C1:
PF118253=Nuc_recep-AF1=PU(65.8=90.4)
A:
NA
C2:
PF118253=Nuc_recep-AF1=PD(32.5=69.8),PF0010513=zf-C4=PU(15.7=20.8)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCCCCTTCTCCTCCAGGA
R:
GTCCCCGCAGATTGCACATAG
Band lengths:
344-843
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]