DreALTA0015725-2/2 @ danRer10
Alternative 3'ss
Gene
ENSDARG00000006896 | lhx6
Description
LIM homeobox 6 [Source:ZFIN;Acc:ZDB-GENE-041025-1]
Coordinates
chr10:9542538-9555273:+
Coord C1 exon
chr10:9542538-9542659
Coord A exon
chr10:9555053-9555055
Coord C2 exon
chr10:9555056-9555273
Length
3 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
AGCTCTTCTCTGTCTCACAGTAG
3' ss Score
7.06
Exon sequences
Seq C1 exon
GTTAATAATCTGATCTGGCACGTGAGGTGTCTGGAATGTTCCGTCTGCAGGACTTCACTACGCCAGCACAGCAGCTGCTATATTAAAAACAAGGAAATCTTCTGTAAAATGGATTATTTCAG
Seq A exon
TAG
Seq C2 exon
GTTTGGTACAAAGTGTGCCCGCTGTGGCCGGCAGATCTACGCCAGCGACTGGGTCAGACGAGCCAGAGGAAACGCTTATCATCTGGCCTGCTTCGCCTGCTTCTCCTGCAAACGGCAGCTGTCCACCGGAGAAGAGTTCGGACTGGTGGAGGAAAAAGTGCTCTGTCGGATTCACTACGACACTATGGTGGAGAACCTGAAACGGGCCGCTGAGAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006896-3-4,3-3-2/2
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=0.000
Domain overlap (PFAM):
C1:
PF0041217=LIM=FE(69.0=100)
A:
NA
C2:
PF0041217=LIM=PD(3.4=2.7),PF0041217=LIM=WD(100=78.7)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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:
GTCTGCAGGACTTCACTACGC
R:
CGGGCACACTTTGTACCAAAC
Band lengths:
101-104
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]