BtaALTA0025894-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000017851 | RXRA
Description
retinoid X receptor, alpha [Source:HGNC Symbol;Acc:HGNC:10477]
Coordinates
chr11:105997303-106004390:+
Coord C1 exon
chr11:105997303-105997482
Coord A exon
chr11:106004221-106004228
Coord C2 exon
chr11:106004229-106004390
Length
8 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
GACCCCCTACCCCGCCTCAGCCG
3' ss Score
2.55
Exon sequences
Seq C1 exon
GCAAGCACTACGGGGTGTACAGCTGCGAGGGCTGCAAGGGCTTCTTCAAGCGGACGGTGCGCAAGGACCTGACCTACACCTGCCGGGACAACAAGGACTGCCTGATTGACAAGCGGCAGCGCAACCGCTGCCAGTACTGCCGCTACCAGAAGTGCCTGGCCATGGGCATGAAGCGCGAAG
Seq A exon
CCGTGCAG
Seq C2 exon
GAGGAGCGGCAGCGGGGCAAGGACCGGGGCGAGAGCGAGGTGGAGTCCAGCAGCAGCGCCAACGAGGACATGCCAGTGGAGAAGATCCTGGAGGCCGAGCTGGCCGTCGAGCCCAAGACCGAGACCTACGTGGAGGCGAACGTGGGGCTGAACCCCAGCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000017851-5-5,5-4-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.544
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(82.9=95.1)
A:
NA
C2:
PF0010425=Hormone_recep=PU(2.1=7.0)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
AGTACTGCCGCTACCAGAAGT
R:
CTGGACTCCACCTCGCTCTC
Band lengths:
98-106
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development