DreINT0129996 @ danRer10
Intron Retention
Gene
ENSDARG00000004697 | rxrgb
Description
retinoid X receptor, gamma b [Source:ZFIN;Acc:ZDB-GENE-040718-34]
Coordinates
chr20:34012773-34013224:+
Coord C1 exon
chr20:34012773-34012864
Coord A exon
chr20:34012865-34013118
Coord C2 exon
chr20:34013119-34013224
Length
254 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAAT
5' ss Score
3.53
3' ss Seq
CCAACTGTATTTTTTCATAGACG
3' ss Score
6.85
Exon sequences
Seq C1 exon
GGTACTGACCGAACTGGTGTCTAAAATGAAGGACATGCAGATGGATAAGACAGAACTAGGCTGCCTTAGGGCCATCGTCCTCTTCAACCCTG
Seq A exon
GTGAATTTGGGTTTTTATATATATATATATATAAAATAAAAAGCAGAAATAAAGGGACAGTTTACCCAAAAAATCTGATTCTTCATGAAGCATATAACCAAAAACATATAACATATATTTATTTATATGTGTGTATGTATGTATTACCGTACACATACCGTATCTTCAATGTAATTACAGTAGATGTAAATTTGACTACATTATGTTGAGAGACCGAACATGTATTCAATCACACCAACTGTATTTTTTCATAG
Seq C2 exon
ACGCCAAAGGCTTGTCAAACTCACTGGAGGTGGAGGCACTGAGGGAGAAGGTTTACGCCTCGCTGGAGACCTACACTAAACAGAAATACCCCGACCAGCCTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004697:ENSDART00000002554:8
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=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(15.8=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(17.9=100)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGAACTGGTGTCTAAAATGAAGGA
R:
GCTGGTCGGGGTATTTCTGTT
Band lengths:
183-437
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]