DreALTD0010892-1/3 @ danRer10
Alternative 5'ss
Gene
ENSDARG00000020354 | lmx1a
Description
LIM homeobox transcription factor 1, alpha [Source:ZFIN;Acc:ZDB-GENE-041014-332]
Coordinates
chr20:34021357-34030744:+
Coord C1 exon
chr20:34021357-34021471
Coord A exon
NA
Coord C2 exon
chr20:34030524-34030744
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
CTTTTGTTTTGTCCTGTCAGGCT
3' ss Score
8.83
Exon sequences
Seq C1 exon
ATCGACACGATGCTCGGACCCCCTCGGCTACCCCAAAACTCAGTCTGATTCACATTCTCACCTCCAAATGCGAAAAAGTCTGCCAAACGACCGAGCGTGATCGACGTTAGTAAAG
Seq A exon
NA
Seq C2 exon
GCTGTTTGTGGTGCGGTGTCAGGGCTGCTCAGAGATCATCTCTCCGTCTGAGCTGGTGATGCGCGCACAGGGCTCTGCTGTTTTTCACCTGCGCTGCTTCTGCTGCTGTGTGTGCGGCTGCCGGCTGCAGAAGGGAGATCACTGTGTGCTCCGAGGAGACGGCCTCTTCTGTGCCACACACTTCCACAACCAACTGGCCAGTCCCACCTCCTCTGACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020354-2-4,3-4,4-4-1/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.108
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0041217=LIM=WD(100=83.6),PF074236=DUF1510=PU(13.2=25.5)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
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:
AAAGTCTGCCAAACGACCGAG
R:
CATCACCAGCTCAGACGGAG
Band lengths:
102-108
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]