DreINT0129972 @ danRer10
Intron Retention
Gene
ENSDARG00000078954 | rxrba
Description
retinoid x receptor, beta a [Source:ZFIN;Acc:ZDB-GENE-980526-436]
Coordinates
chr19:7351072-7353410:-
Coord C1 exon
chr19:7353274-7353410
Coord A exon
chr19:7351302-7353273
Coord C2 exon
chr19:7351072-7351301
Length
1972 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TCTTTTGTCTGTCTTCACAGATT
3' ss Score
11.43
Exon sequences
Seq C1 exon
GGATCACTTCGGTTGGTAAAAGATCCAAAGGCCCGGGCCTCAGTCCGCGGTCTTGAGTTCGACAGCCACCCGACATCAGAGCGAGAGAGTCGGTGTGAACAGCAGAGCCCGGCTGCACAACATGGGCGACAGCAGAG
Seq A exon
GTGAGACTGTTTTGCTTTTATACCTACATGTGGCTCCATGTTTACGCGGTGAAATTTACACTTGGAGTTGTAAACTTTTTAATTGCCATTTCTAAGGTTTAATAGCCAGAATATGATTTTTATATGACTGTAGTATTGTTAAGGTGGTTAATTTATATAGCTTTGTTTGCCTGAGTTCTATTACAGAAGACAAACCTTTGCACAAGGCCCGCAAAAATTTAGGAATCTTTATCTCTGGCTATTTAGTGTAGTGTATTTATTTATTTTTATTCATTAAAATATTTTATGACTAATTTTAGGTAAAACTGTGATAACCTAATGTTTTTAAAATACACGTCAAGCCACTGTATCTGAAATTTGAGAATTAAAAAAGATGAATACAGGTATACAAGATTAACACTTGTGGCTCCTGTTAATATATTGTGACCTTGTAAAGGGAAATGTTCGATCAGTGCAAGAAACTGAACATTTATTACAACATTATTACATCCACAGCGTAATGATTTACATGGCAATCTGGAGCATACGCTTAAAAAATATATTGTGCGTAGTTAAATTTGCTTTCAAGCTCTTGCTGTTTGTTTACAATTGTGAGAAAGAACACATTAATAGTATTGTTATCAAGCATATCAGTACTGAAGACAGAAATTGAATAATCACAATGCAAAATGATTTCCCAAAATTTTTAGTCCAAATATCTAAACAATTTCAATCAAGTAAAAAATTGTTTTGTTTTCAACTTTAGAAGAAATAAATAAAAATTAAGCATTTTTATTCTTAAAGCAAGTCAAAGTGGAATAAGTAATATAATCTTGTTTTCACTTTAAAATGTAGATATTTGGACAAGAAACAACAAAAATTAAAGTTAGACTTTTTTCTTCTTCGTTTATTAAATGGTATAAATACAATAATTAAATACATTTTTTTAGCTCCTGGTAAAATAGAATTCAGACTCAAATTTGCACACTGTGTGATGCATTACATTACGATATCTGTGCTGAAATGATATATTATGCAGCCATAATTTTTAATCTAAATGGTATTTACTTGTGCTCTTGCTCCAGACTGCCATTATCAACTATGGTGTAGTGTGGCAAGGCTGTAGATTAAAGGATTAGGGCTGGGTCATTATCAATAGCTGTCAAGGTAAATGTCAAATCTCTATTTCATTCCAATTTAAAGGTGTATTTTTGCTTTTGAGTGTGAGTTTTAGAAACCAGATTTTTCATTTTTACTTCAACTCTTATATTGTAAAAATGTGACAAACAAGTCAACTAGATAGACATTTGACAAATCTGACTTGCAATGTATCAGTATTTATAAAATGTATAAATATTAACTTAAAATCTTTATAAGAGAAATGATTTTCCTAATTTCAGCATGTTCTAATATTTATATCAAATCCTATAACAGTTTGTTTTCTGACTTAAAAGGCACAATGCAGATGTGAATTTATGTTCAGTAAAATAAAAACAAACATGATCAAATATTTAAATAGTGTGTGTGCTTGATTTTAGTAATCTTAAATATTGTTATATCTAATATCATCCATCTTGAAATGTAACTGGTTTGGTGTTTATGATGATTGGTCAAATATATTAAGAATAAATAGGAATACTGTTGCTTTTTCTGGGCGAAATTATGTAGCGATACATTATCGTTACTGTTTTATCGCCTAGCCGTTCTATAAATAATATTCAGTTTCTTGCACAGGCTGATCGTTTTGCTTCATAAGACCGCAGTGTATCATCAGGAGCCTCAGGTATTTATTTTGTTTGCCTGTATAATTTTTTTTCATTTAATGAATCACTAAAAGGTCACAATTTCAGATTAAAATCTTTTTGTGTTGTTCTAATCTACGGATGCTTTTGGATGGCCCGAGGGAGAGTAAATTAAAATAAGCCATGTATCATCTATTTAAATTGATTGTCCAGTTTGTATTCAGTGTATAATCTTTTGTCTGTCTTCACAG
Seq C2 exon
ATTCTCGTAGTCCAGACAGTTCATCCGTTTCCTCACCACCATCAGGTCAGCGTTCGCCCCCGTTGGCCCCGTCAGCTGCCGCCATGACTTCTCTCCCACCCATCACTTCGGCTGTGAACAGCCCCATCAGCAGCATGGGCTCACCCTTCTCGGTCATCAGCTCATCCCTGGGGTCTCCTTGCCTTCCTGGAACTCCCTCGGTGGGCTACGGCCCCATCAGCAGCCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000078954:ENSDART00000009755:2
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=0.426
Domain overlap (PFAM):
C1:
PF118253=Nuc_recep-AF1=PU(0.1=0.0)
A:
NA
C2:
PF118253=Nuc_recep-AF1=PU(67.3=98.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAAAAGATCCAAAGGCCCGGG
R:
CTGTGGGCTGCTGATGGG
Band lengths:
351-2323
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]