GgaINT1016828 @ galGal4
Intron Retention
Gene
ENSGALG00000000936 | LMX1B
Description
LIM/homeobox protein LMX-1.2 [Source:RefSeq peptide;Acc:NP_990689]
Coordinates
chr17:10059278-10059758:+
Coord C1 exon
chr17:10059278-10059347
Coord A exon
chr17:10059348-10059568
Coord C2 exon
chr17:10059569-10059758
Length
221 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CGCGCTTTGCCGTTTCGCAGGGT
3' ss Score
9.34
Exon sequences
Seq C1 exon
ATGCTGGACGGCATCAAGATGGAAGATCACCCGCTGCGCTCGGGTCCGGCCACGCTCGGAGTGTTACTGG
Seq A exon
GTGAGTCCCGCTCGCTCCTCGGCCGTGCCCCAGAGCAGGCGCTCCGCGGCTCCGCGCCGTCCCGGGCTGCGCCGTGCGGGGCTGACCGCGCGCTGCGGGCGCGGGACTGTGAGTGACACTTCGGGGCGCGCGCCGGGAGCGGCCGCTCCGCGCGGTGCTGCCGAGCGCGGGACCCGGGGGGCCGTCCCCGCCGCCTCACGCCGCGCTTTGCCGTTTCGCAG
Seq C2 exon
GGTCGGGAGTGCCCCGCATCCAGGCCGTGTGCGAAGGCTGCCAGAGGCCCATCTCGGATCGCTTTCTGATGAGGGTGAACGAGTCCTCCTGGCACGAGGAGTGTTTGCAGTGCGCGGTGTGTCAGCAAGCCCTCACCACCAGCTGCTACTTCCGGGACCGAAAGCTCTACTGCAAACAGGACTACCAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000936:ENSGALT00000001376:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=82.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGACGGCATCAAGATGGAAG
R:
TGTTGGTAGTCCTGTTTGCAGT
Band lengths:
256-477
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]