DreEX0063829 @ danRer10
Exon Skipping
Gene
ENSDARG00000057737 | rxraa
Description
retinoid X receptor, alpha a [Source:ZFIN;Acc:ZDB-GENE-070314-2]
Coordinates
chr21:17780975-17872624:+
Coord C1 exon
chr21:17780975-17781085
Coord A exon
chr21:17843906-17844144
Coord C2 exon
chr21:17872474-17872624
Length
239 bp
Sequences
Splice sites
3' ss Seq
TTCTGCTTTCCTCCCCACAGACT
3' ss Score
12.38
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
Exon sequences
Seq C1 exon
GGTTCCTGAAGCCCCAGTGCTCACTACCGCCGCCACCTCAGAGAGGACGAGCAGAAGCATGTACGTGTTTCAGCGGAATGTGTGCTCTTCATCAACGCAGGCTTTCTACAG
Seq A exon
ACTGCACTGGACAGGTGACATCCTCTCCTCTCAGCTCACCCACGTCCCACCGGGGCATGCACCCGTCACTGCTGAGTCCAACTTCATTAGGCCCCTCGGGGTCCCTGCACTCCCCCATCAGCACTCTGAGCTCACCTATGAATGGCCTGGGCTCTCCCTTCTCCGTCATCAGCTCGCCTATGGGGCCTCATTCAATGGCATCTCCTGGAGTGGGTTACGGCCCCAGTATCAGCCCTCAG
Seq C2 exon
TTGAACTCGCCCATGAACTCTGTCAGCAGCTCAGAGGATATTAAGCCGCCCTTAGGCCTCAACGGTGTGATGAAGGTTCCAGCCCAGCCCTCGGGCACCCCACTCTCTCTCACCAAACACATCTGTGCCATCTGTGGCGACCGCTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000057737_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.158 A=0.810 C2=0.593
Domain overlap (PFAM):
C1:
NO
A:
PF118253=Nuc_recep-AF1=PU(68.8=96.2)
C2:
PF118253=Nuc_recep-AF1=PD(29.5=64.7),PF0010513=zf-C4=PU(15.7=21.6)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCCTGAAGCCCCAGTGC
R:
CTGAGGAGCGGTCGCCAC
Band lengths:
261-500
Functional annotations
There are 1 annotated functions for this event
PMID: 11162439
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: mutation analysis, protein kinase assay. ELM ID: ELMI001406; ELM sequence: GRGSMAA; Overlap: FULL
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]