GgaINT0126114 @ galGal4
Intron Retention
Gene
ENSGALG00000003928 | LIM3
Description
LIM/homeobox protein Lhx3 [Source:UniProtKB/Swiss-Prot;Acc:P53412]
Coordinates
chr17:8046967-8047518:+
Coord C1 exon
chr17:8046967-8047138
Coord A exon
chr17:8047139-8047315
Coord C2 exon
chr17:8047316-8047518
Length
177 bp
Sequences
Splice sites
5' ss Seq
CAAGTGCGT
5' ss Score
6.68
3' ss Seq
CCGTCTGTCGCCCCACTCAGACG
3' ss Score
6.46
Exon sequences
Seq C1 exon
AGATCCCGCTGTGCGCCGGCTGCAATCAGCACATCGTGGACAGGTTCATCCTCAAGGTCCTGGACCGGCATTGGCACAGCAAGTGCTTGAAATGTTCCGACTGCCAGACGCAGCTGGCCGAGAAGTGCTTCAGCCGAGGGGACGGCGTGTACTGCAAGGAGGATTTCTTCAA
Seq A exon
GTGCGTGGGCCGGGGGGCGGCGGAGGGGAACCGGGGGGGCGGAGGGGAACCGGGGGGCGCTCAGCCCCGTGGACGGTGGCTCCGTCCCGGGGTTCAGCACCGCGGACAGCGGCCGCTCTCGGGCTCAGCCCGCGCGGCTCTCCGCGCTCAGCGGCCGCCGTCTGTCGCCCCACTCAG
Seq C2 exon
ACGCTTCGGGACGAAGTGCGCCGCCTGCCAGCAGGGCATCCCCCCGACCCAGGTGGTGCGCCGGGCCCAGGACTTCGTGTACCACCTGCACTGCTTCGCCTGCATCGTCTGCAAGCGGCAGCTGGCCACCGGAGATGAGTTCTACCTGATGGAGGACAGCAGGCTGGTGTGCAAGGCTGACTACGAGACGGCCAAGCAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003928:ENSGALT00000002663:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.014
Domain overlap (PFAM):
C1:
PF0041217=LIM=PU(94.6=91.4)
A:
NA
C2:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCCGAGAAGTGCTTCAG
R:
GTCTCGTAGTCAGCCTTGCAC
Band lengths:
248-425
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]