BtaINT0127971 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000602 | RXRB
Description
Bos taurus retinoid X receptor, beta (RXRB), mRNA. [Source:RefSeq mRNA;Acc:NM_001083640]
Coordinates
chr23:7323163-7324636:-
Coord C1 exon
chr23:7324457-7324636
Coord A exon
chr23:7323336-7324456
Coord C2 exon
chr23:7323163-7323335
Length
1121 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
TCCTTCCCCCTCCCCCTTAGCTG
3' ss Score
8.38
Exon sequences
Seq C1 exon
GCAAACACTACGGGGTTTACAGCTGCGAGGGCTGCAAAGGCTTCTTCAAGCGCACCATCCGTAAGGACCTGACCTACTCGTGCCGGGACAACAAGGACTGCACGGTGGACAAGCGCCAGCGGAACCGCTGTCAGTACTGCCGCTACCAGAAGTGCCTGGCTACTGGCATGAAGAGGGAGG
Seq A exon
GTAAGGGCCTGCCCCAGGCCTCCCCTTGTGTCCTGTGGGAGGAGGGGGAGGGAGCACTTCCGGGTCCGCCCTCTCTGGAAGGCGGGGCCCCTCTCTCTCCTCCAGAGGGCGCTGTTTCACTCATCTCTCCCATGCACATTCGCTCTCCTCCCTGGTACCCCGATCTGGTCCCTTGAGTTTCCTTGTTAATGGATCTGCCACTCTGGCCTGAACCTCTGACCACCACCCACCCCCCTCACCCCAGGCTGGTGCTAGGATCACTTTTACTTCTCCAGGATGGTTTCTCTAGCTCCCCCTCTCTAACCGGATTAGCTTTTCTTCTCTTTGAACCCACCTTCCACTCTGGCCTCTGTCTCCGTGGTATCTGTGTTGGCTTCTCCAAACTCTGGGACTGTGCTCTCTTAAACTGCAGCCTTTACTAAAAGACTCCCAAAACATCTTTCCTCTTTTTTCTCTCTGTTTTATCTTAGTCTGATTCTGAAATCCTGAGAGAGATGCTTTAGGGAGTTTATGTTGGTCACCTGCCTCATTTTAGAGAAGATGAGCTTGAAGCCTGGCTTTCCCAAGGTCATGCAACAAAAGAGTGACAGGTCTGGGATCAGAATCCATGTCCCTGAAGACCCAGGCCCAGTGCGCCTTCTCCTGCCACTTGGTTGAGTCGGAAGAACACCAGATTTGCAGTTAGGAACACTTAGGTTTACATGTATGATGTGCCATGTATTGTGTGAACTTGGACAAACTGTTTTAATGAACTGCCTCAAAATCAATATCTTTAAAAACGGGGTCAAGAGCTCACAGGGTGGTTATAAATACTGGAATGAATGTTAAAGCACGCTTGGCATGTTTTTTAGTATGTAGAAGGCCTTCTGTTTAAATGTTAGTTTTCTGCTAATTTCTCTGTCCACCTCTTTTACTTCTTGGAGTAGTCATCTGTTCTTTCATAACTCCTGTGTCTAGACTGCCACAAATATGCCGTGGTTTCAAGTGACTTCCCCAATTTCTATAAATATCTTCTGAGTTAGGCCAGGAGACCCCGATATGGCCCTAAGGACACTTTGGAATCTCCTCACGGCTGGCTACTGACTCTCCATTTTTCTCTCCTCCTTCCCCCTCCCCCTTAG
Seq C2 exon
CTGTACAGGAGGAGCGTCAGCGGGGGAAAGACAAAGACGGGGATGGGGAGGGTGCTGGGGGAGCCCCCGAGGAGATGCCTGTGGACAGGATCCTGGAGGCAGAGCTTGCTGTGGAGCAGAAGAGCGACCAGGGCGTGGAGGGTCCCGGGGGGACCGGGGGCAGCGGCAGCAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000602:ENSBTAT00000000860:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.845
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(82.9=95.1)
A:
NA
C2:
PF0010425=Hormone_recep=PU(0.1=0.0)
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:
CAAACACTACGGGGTTTACAGCT
R:
CTGGTCGCTCTTCTGCTCCA
Band lengths:
310-1431
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]