DreALTA0015866-2/2 @ danRer10
Alternative 3'ss
Gene
ENSDARG00000077915 | lmx1al
Description
LIM homeobox transcription factor 1, alpha-like [Source:ZFIN;Acc:ZDB-GENE-131213-1]
Coordinates
chr3:52555035-52560576:+
Coord C1 exon
chr3:52555035-52555120
Coord A exon
chr3:52560369-52560392
Coord C2 exon
chr3:52560393-52560576
Length
24 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGA
5' ss Score
8.94
3' ss Seq
TATTTGTGTCCTGGCGTCAGCTG
3' ss Score
3.55
Exon sequences
Seq C1 exon
TCAGCACTCCAAAGAAGGAAGGAGCGGAATGAAAACAGAAGAAAACCAGTCATGTCTTCAGCAGGCCCCCTCCGCCACACCTTACG
Seq A exon
CTGACTCCTGTTCTCCTCCACCAG
Seq C2 exon
ACCATGTGGGAGGAGGTGAGGTGTGCGCAGGCTGCGAGTCCCCCATCGCGGACCGGTTCCTGCTGCGCGTCAATGAACTGTCCTGGCATGAGACCTGTGTGAAGTGTGCGGTGTGTCGCAGCGCTCTGAGCGGGACCTGCTACTGTCGGGACAGACTGCTCTACTGCAAGCACGATTACGAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077915-1-2,1-1-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.067 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=85.5)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
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:
TCCAAAGAAGGAAGGAGCGGA
R:
CACCTCACCTCCTCCCACAT
Band lengths:
102-126
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]