GgaINT0126115 @ galGal4
Intron Retention
Gene
ENSGALG00000003928 | LIM3
Description
LIM/homeobox protein Lhx3 [Source:UniProtKB/Swiss-Prot;Acc:P53412]
Coordinates
chr17:8047316-8047823:+
Coord C1 exon
chr17:8047316-8047518
Coord A exon
chr17:8047519-8047671
Coord C2 exon
chr17:8047672-8047823
Length
153 bp
Sequences
Splice sites
5' ss Seq
GAGGTACGG
5' ss Score
9.4
3' ss Seq
AACCCGCGTCGTGCCGGCAGAGG
3' ss Score
5.54
Exon sequences
Seq C1 exon
ACGCTTCGGGACGAAGTGCGCCGCCTGCCAGCAGGGCATCCCCCCGACCCAGGTGGTGCGCCGGGCCCAGGACTTCGTGTACCACCTGCACTGCTTCGCCTGCATCGTCTGCAAGCGGCAGCTGGCCACCGGAGATGAGTTCTACCTGATGGAGGACAGCAGGCTGGTGTGCAAGGCTGACTACGAGACGGCCAAGCAGAGAG
Seq A exon
GTACGGAGCGCCCTTCGCCCCCGGGGAAGAGAGAGGCGGCTCCGGGCCGCGCTGCCCTCGGGGCTCCGCTCGTGCATAGGGTTGGGCAGGAGGGAGGGCGGGGGTCCCGGGTCCGCACGGGGAGCTGCGAGCTAACCCGCGTCGTGCCGGCAG
Seq C2 exon
AGGCCGAGTCCACGGCCAAGAGGCCCCGCACCACCATCACAGCCAAGCAGCTGGAGACCCTCAAAAACGCCTACAACAACTCGCCCAAGCCGGCGCGGCACGTCCGGGAGCAGCTCTCGTCGGAGACGGGGTTGGATATGCGGGTGGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003928:ENSGALT00000002663:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.765
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=86.3)
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:
CTTCGTGTACCACCTGCACTG
R:
TCTCCGACGAGAGCTGCTC
Band lengths:
257-410
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]