HsaALTA1014135-2/3 @ hg38
Alternative 3'ss
Gene
ENSG00000106852 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:HGNC:21735]
Coordinates
chr9:122214287-122217288:-
Coord C1 exon
chr9:122217068-122217288
Coord A exon
chr9:122214384-122214436
Coord C2 exon
chr9:122214287-122214383
Length
53 bp
Sequences
Splice sites
5' ss Seq
ACGGTACCC
5' ss Score
6.32
3' ss Seq
CCCACCCCCGTCCTTTCCAGGCT
3' ss Score
10.11
Exon sequences
Seq C1 exon
CCGATTCGGGACCAAGTGTGCCCGGTGCGGCCGACAGATCTACGCCAGCGACTGGGTGCGGAGAGCTCGCGGCAACGCCTACCACCTGGCCTGCTTCGCCTGCTTCTCGTGCAAGCGCCAGCTGTCCACTGGTGAGGAGTTCGGCCTGGTCGAGGAGAAGGTGCTCTGCCGCATCCACTACGACACCATGATTGAGAACCTCAAGAGGGCCGCCGAGAACG
Seq A exon
GCTGCCACTAGAAGAGATGGGGACGCGTGGTCAGCTGCTTCTATCGCCCCCAG
Seq C2 exon
GGAACGGCCTCACGTTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAACCCAAGCCGGCCAAGCGCGCGCGGACGTCCTTCACCGCGGAACAGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000106852-14-16,14-15,14-14-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.026 A=NA C2=0.845
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.4=2.7),PF0041217=LIM=WD(100=77.3)
A:
NA
C2:
PF0004624=Homeobox=PU(21.1=35.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGTCGAGGAGAAGGTGCTC
R:
GCTTGGGTTGACTGTCCTGTT
Band lengths:
133-186
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains