DreALTA0023599-2/2 @ danRer10
Alternative 3'ss
Gene
ENSDARG00000057737 | rxraa
Description
retinoid X receptor, alpha a [Source:ZFIN;Acc:ZDB-GENE-070314-2]
Coordinates
chr21:17873782-17879973:+
Coord C1 exon
chr21:17873782-17873961
Coord A exon
chr21:17879789-17879803
Coord C2 exon
chr21:17879804-17879973
Length
15 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
ACTGTAGTGACCGTGACTAGTAT
3' ss Score
-0.34
Exon sequences
Seq C1 exon
GTAAACACTACGGTGTGTACAGCTGCGAGGGATGTAAGGGTTTCTTCAAGAGGACAGTGCGTAAAGACCTGACCTACACCTGTCGAGACAATAAGGACTGTGTTATAGACAAACGCCAGCGCAACCGCTGCCAGTACTGCCGCTATCAGAAGTGTTTGGCCATGGGCATGAAGAGAGAAG
Seq A exon
TATTATTACATACAG
Seq C2 exon
CCGTCCAGGAGGAGCGCCAGCGAGCCAAGGAACGCAGTGAGAACGAAGTGGAGTCGACCAGCAGCGCCAATGAAGACATGCCCGTGGAGAAGATACTGGAAGCAGAGCTTGCTGTGGAGCCCAAGACGGAAACTTACATTGAGACTAATGTACCCATGCCATCAAATTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000057737-9-12,9-11-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.632
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(82.9=95.1)
A:
NA
C2:
PF0010425=Hormone_recep=PU(11.9=21.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGTACTGCCGCTATCAGA
R:
TGGTCGACTCCACTTCGTTCT
Band lengths:
111-126
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]