DreINT0129992 @ danRer10
Intron Retention
Gene
ENSDARG00000004697 | rxrgb
Description
retinoid X receptor, gamma b [Source:ZFIN;Acc:ZDB-GENE-040718-34]
Coordinates
chr20:34007757-34008647:+
Coord C1 exon
chr20:34007757-34007936
Coord A exon
chr20:34007937-34008486
Coord C2 exon
chr20:34008487-34008647
Length
550 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTGC
5' ss Score
5.38
3' ss Seq
ATATTTATATTTCCCCACAGCGG
3' ss Score
10.26
Exon sequences
Seq C1 exon
GGAAGCATTATGGTGTTTATAGTTGTGAAGGCTGCAAGGGCTTCTTTAAGAGGACCATTCGAAAAGACCTGACGTACACATGTCGAGACATTAAAGAGTGCCTGATCGACAAGCGCCAGCGCAACCGCTGCCAATACTGCCGCTACCAGAAGTGCTTGGCCATGGGCATGAAGCGCGAAG
Seq A exon
GTCTGCATTGGTTTTGAGTAAACTGTTTATATTATGAATGTTGTATTAAATTATTTTGAAGTATATTTTTGGTAAAGTAAATAGAATAAAAATAAAAAGTATATATAAACAATATTTTAAATAAATAAATAGAATATATTTTAGTATAAATCATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATGTGTGTGTGTGTGTGTGTGTATGTATGTATGTATGTATGTGTGTGTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATGTATGTATATATATAAAGTTTTTTCTTTATTATTATGCAAAAATTTGCAAAAGAAATTTCAACAAGATCTGATCAAGAACAAATTGTATTTTTTTGCTTCATTACTACAATGTTAAATAACACAAAAGTTCTTATATTATGTACAAAAATATTTAAGATGCAACAAAATAAAATAAAAATCATAAAATATATTTATATTTCCCCACAG
Seq C2 exon
CGGTTCAGGAAGAGAGGCAGCGAGGGAAAGAGAAAAGTGATACTGAGGTGGAAACAACAAGCAGGTTTAATGAAGACATGCCTGTGGATAAAATCCTGGATGCAGAACTGTCAGTCGAACCCAAGACTGAGACGTACACAGAGAGCAGCCCCAGCAACTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004697:ENSDART00000002554:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.593
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(82.9=95.1)
A:
NA
C2:
PF0010425=Hormone_recep=PU(6.6=24.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAGCATTATGGTGTTTATAGTTGT
R:
CTGGGGCTGCTCTCTGTGTA
Band lengths:
334-884
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]