GgaINT0124506 @ galGal4
Intron Retention
Gene
ENSGALG00000001347 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:HGNC:21735]
Coordinates
chr17:8725622-8725894:-
Coord C1 exon
chr17:8725794-8725894
Coord A exon
chr17:8725718-8725793
Coord C2 exon
chr17:8725622-8725717
Length
76 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTG
5' ss Score
6.13
3' ss Seq
CTCTCCTTGCCACCCACCAGGTC
3' ss Score
7.51
Exon sequences
Seq C1 exon
GCAATGGGATCACACTGGAGGGGGCCGTGCCCTCAGAGCAGGACAGCCAGCCAAAGCCAGCCAAAAGGGCCCGCACCTCCTTCACCGCTGAGCAGCTGCAG
Seq A exon
GTAGTGGGGCTGGGCCAGGGCTGGGAGGGGCTGCGGTGTCAGCCACAACCTGACCCCTCTCCTTGCCACCCACCAG
Seq C2 exon
GTCATGCAGGCACAGTTTGCTCAGGACAACAACCCCGATGCACAAACGCTTCAGAAACTCGCAGACATGACGGGGCTGAGTCGGAGAGTCATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001347:ENSGALT00000002057:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.824 A=NA C2=0.656
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(21.1=35.3)
A:
NA
C2:
PF0004624=Homeobox=FE(54.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAATGGGATCACACTGGAGG
R:
TGTCTGCGAGTTTCTGAAGCG
Band lengths:
168-244
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]