GgaINT1016696 @ galGal4
Intron Retention
Gene
ENSGALG00000001735 | LHX4
Description
LIM homeobox 4 [Source:HGNC Symbol;Acc:HGNC:21734]
Coordinates
chr8:5961215-5961660:-
Coord C1 exon
chr8:5961458-5961660
Coord A exon
chr8:5961370-5961457
Coord C2 exon
chr8:5961215-5961369
Length
88 bp
Sequences
Splice sites
5' ss Seq
ACGGTAGGC
5' ss Score
8.81
3' ss Seq
CGCCACTCATTTGCTCCCAGATG
3' ss Score
6.94
Exon sequences
Seq C1 exon
GCGCTTCGGGACCAAATGCACGGCGTGCCAGCAGGGCATCCCCCCCACGCAGGTGGTGCGCAAAGCCCAGGACTTCGTCTACCACCTGCACTGCTTCGCCTGCATCATCTGCAGCCGGCAGCTGGCCACCGGCGACGAGTTCTACCTGATGGAGGACGGGAGGCTGGTGTGCAAGGAGGACTACGAGACTGCCAAGCAGAACG
Seq A exon
GTAGGCACGGCCCCCAAGCTCGCGTTTTATGGCCCCCCAAGCTCGTGTTTTACTGCCGGGGCTGCTCACGCCACTCATTTGCTCCCAG
Seq C2 exon
ATGACTCCGAGGCGGGGGCTAAGCGGCCCCGCACCACCATCACAGCCAAGCAGCTGGAGACGCTGAAGAATGCCTACAAGAATTCCCCCAAGCCTGCACGGCATGTGCGGGAGCAGCTCTCCTCCGAGACGGGGCTGGACATGAGAGTGGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001735:ENSGALT00000035845:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.654
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
A:
NA
C2:
PF0004624=Homeobox=PU(77.2=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGACGAGTTCTACCTGATGG
R:
CAGGCTTGGGGGAATTCTTGT
Band lengths:
168-256
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]