DreINT0129973 @ danRer10
Intron Retention
Gene
ENSDARG00000078954 | rxrba
Description
retinoid x receptor, beta a [Source:ZFIN;Acc:ZDB-GENE-980526-436]
Coordinates
chr19:7348960-7351301:-
Coord C1 exon
chr19:7351072-7351301
Coord A exon
chr19:7349114-7351071
Coord C2 exon
chr19:7348960-7349113
Length
1958 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTCATCATCATCCTCCTCAGATC
3' ss Score
7.94
Exon sequences
Seq C1 exon
ATTCTCGTAGTCCAGACAGTTCATCCGTTTCCTCACCACCATCAGGTCAGCGTTCGCCCCCGTTGGCCCCGTCAGCTGCCGCCATGACTTCTCTCCCACCCATCACTTCGGCTGTGAACAGCCCCATCAGCAGCATGGGCTCACCCTTCTCGGTCATCAGCTCATCCCTGGGGTCTCCTTGCCTTCCTGGAACTCCCTCGGTGGGCTACGGCCCCATCAGCAGCCCACAG
Seq A exon
GTGAGCAGCTTTTCAGCAGGGTTTCATTCTGTGTGGAGGGCACTCAAAGAAAAAGAGTTCAGCTTGTTTTTGCCATCAGGATATTTTTAGAACATGATCATACTAGATTTAAGTCACCTTCTTTCTTTTTTTAAAGGTTACAGTTAGAAAGCTGCACAGTAGATCACTCAAAAATGAAAAACAAATTATTTAATAACCTGTCAAGTGCTTATAAATCTTAATCTACCATGATAATACTAGATTTTCTACCATGATAATACCATGATGATATTAGATTTTTATGTCTATGTTTTGTATCTAGATAATAAAGTAGATACACAGTAGGTGAAGGATAGCTCACTCAAAAATAAACTCATTTACACCCCCTCAGGTGGTTGTATATCTTCATCTACCATGATAATACTAGATTTTCTACCATGATAATACTAAAGTCTATTTTTCTATTTATATCATGGAGATTGCAGTCAGAAAGCTGCACTGTAGATAAAGGCATAGTTCACTCAAAAAAGAAAGTTTACTCATTTAATATCCCTCAAGCGGTTATAAATGTAAATCTACCATTATAATACTAGATTTATACCATGATAATACCATGATAGTACTAGATTTATGTCATGTTATTTTATTTAGATGATGATGACAGTCAGAAAGCTGCACGGTAGTTAAAGAGACAGTTCACTCAAATTATAATTAACTCACCATTTACCTCTCCTTGAGTGGTTAAAAGTCTTTGAGTTTCTTTTCTTCGATTGAACACGAGAAGATATTTTGAAGAATGCTGAAAACCTGTTACCATTGACTTCCATAGTTGTAAAAACAAATACTTTTGATGTAAATGGTTGCAGGTTTTTTCAAAATATCATCTTTTGTGTTCAAAACAATTAAGAAACACAAGCCGGTTTTAAACAAGGGAGCGTAAATGAGTGAAATTATTTTTGGGTGAACTATCCCTTTAAGTTATCAGCATTGCGATGTATATTACAGTATAAAGGTTTAAGGTCAGAAAGTTTTTGAGAATAAATACTTATATTAATGAAGCACAAATTTTAATATTAATATGTTTTTTTTAAAAGGATCATGTGAAACTGAGTACAGGAGTAACAGCTGCTTTAAATTTATCTGTAAAATTATATTTTGAACTATATGAAATAAGCTTTTACAAATTTCACAATTACTGTCTTTCAGTACTTGCATTTGTATACAAATTTCTCTATTTATGCGAACAAATTCATTGAAAAAAATCCCAGTTTATTCACCAAGATAATTGTAGCGTTTCCCTCTAAAACTGTTAATCTTTAACAGAGCTTCTGGTATTTTGACCTTAATTTCCAAAGTCTCTCAGGTATGCTTCTGCCGATCTAAGCCAGATTTTTTTTGGCAGTCTAAATTTTACTCTTAACAAACTAAATTTCATAGTGGATTTAGTGATTCTTTAGCAGCTAAACCCTCAATCCAGAAGCTTTTTTTGTGCGCTCCTTATCACTGCATTTCTGCTTCACAGATGAACATGTTTCCCAGAAACGCAGAGGTGAGACCTTGTACCCTCGCTCAGTTCCTCGCTCTCCAATGCTCTTTTTCGTTTTCTAGTCGCTTTTCTTTTGCATATTCTTTTTCTCTTTACTACTGCTGGTAAATGCTCAATTTGGACAATTAAATATCATCTTTTTGTGAAGGGCTGTGTTCAGATTACATCAAAATAAAATCAAAAAAGTTGATCATGTGTTCAGAGGGTTTTATTTGAGATGAAATGCTGCTTGAATGATTTGGGGAGAAATGTCTGGTCATGATCAGTTAATTAATTATCATAAAAAAATTAACATGTATTTTTCTGTTATCGTTTGATTTTTAACACTAACTAAAATGTAAGAATTATGTCATTTATCTATAATTTAATATGCAATTTTTCTGGCACTTTATGTCTGTTTTTCGTCTTGACGTCTCATCATCATCCTCCTCAG
Seq C2 exon
ATCAACTCCACCGTGTCCATGTCAGGTCTGCATGCCGTCAGCAGCTCCGATGACGTGAAGCCACCCTTTGGTTTGAAGCCGCTGTCCTCTCACAGTCCAGGACCCATGGTTTCACAGAAACGCCTGTGTGCCATCTGTGGAGACCGCTCCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078954:ENSDART00000009755:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.426 A=NA C2=0.348
Domain overlap (PFAM):
C1:
PF118253=Nuc_recep-AF1=PU(67.3=98.7)
A:
NA
C2:
PF118253=Nuc_recep-AF1=PD(31.0=67.3),PF0010513=zf-C4=PU(15.7=21.2)
Main Inclusion Isoform:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTAGTCCAGACAGTTCATCCG
R:
CTGTGAAACCATGGGTCCTGG
Band lengths:
342-2300
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]