DreEX0043325 @ danRer10
Exon Skipping
Gene
ENSDARG00000020354 | lmx1a
Description
LIM homeobox transcription factor 1, alpha [Source:ZFIN;Acc:ZDB-GENE-041014-332]
Coordinates
chr20:34031229-34035865:+
Coord C1 exon
chr20:34031229-34031410
Coord A exon
chr20:34033775-34033852
Coord C2 exon
chr20:34035778-34035865
Length
78 bp
Sequences
Splice sites
3' ss Seq
GTCTGTTTGTCTATTGTAAGGTG
3' ss Score
6.01
5' ss Seq
AAGGTAACG
5' ss Score
10.19
Exon sequences
Seq C1 exon
GTAAAAGTGAGGATATTGAGGAGGACAACGATGATGAAGACAACTTGAAGACTGCAGGAGAGTCAAACATAACAGGAGACGTGGAACACAAGAGGCCTAAAAGACCTCGTACCATCCTGACAACACAACAGAGACGGGCTTTCAAAGCTTCTTTTGAGGTTTCATCCAAACCCTGCCGAAAG
Seq A exon
GTGAGGGAGACTCTGGCAGCAGAGACAGGACTGAGCGTACGAGTCGTTCAGGTCTGGTTCCAGAACCAAAGAGCCAAG
Seq C2 exon
ATGAAAAAACTGGTGAGAAGACAACAGCAGCAGAAGCAAACTGTGTGCCCACAGGAGAAGAGGGAGAGTCCATCACAACAACATACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020354_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.697 A=0.000 C2=0.978
Domain overlap (PFAM):
C1:
PF074236=DUF1510=FE(56.6=100),PF0004624=Homeobox=PU(47.4=44.3)
A:
PF074236=DUF1510=FE(23.6=100),PF0004624=Homeobox=FE(43.9=100)
C2:
PF074236=DUF1510=PD(3.8=57.1),PF0004624=Homeobox=PD(3.5=28.6)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGACTGCAGGAGAGTCAAACA
R:
ACAGTTTGCTTCTGCTGCTGT
Band lengths:
178-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]