GgaINT0036059 @ galGal4
Intron Retention
Gene
ENSGALG00000003424 | LMX1A
Description
LIM homeobox transcription factor 1-alpha [Source:RefSeq peptide;Acc:NP_001244317]
Coordinates
chr8:5163273-5163624:+
Coord C1 exon
chr8:5163273-5163442
Coord A exon
chr8:5163443-5163546
Coord C2 exon
chr8:5163547-5163624
Length
104 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
AGATGTTGTTCCTCCTGCAGGTG
3' ss Score
10.01
Exon sequences
Seq C1 exon
GTAAAAGTGACGATGAAGACAGTGTCTGCAAAATGGGCCCAGCCTCAGCGAAGGGAGCTGAGGAGGGGAAGGACCACAAGCGGCCCAAGCGCCCGCGCACCATCCTGACCACGCAACAGCGCAGGGCCTTCAAGGCGTCCTTCGAGGTCTCCTCCAAGCCCTGCAGGAAG
Seq A exon
GTATGGGGACACTGGGGGTGGCCCGGGGGCTGGGCAGTAGCTCTGCCCCCTCCTGGATCCCCAAACCTTGTGTGAGTCCCACTGAGATGTTGTTCCTCCTGCAG
Seq C2 exon
GTGCGGGAGACACTGGCAGCCGAGACAGGGCTGAGCGTGCGCGTGGTGCAGGTCTGGTTCCAGAACCAGAGAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003424:ENSGALT00000005411:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.596 A=NA C2=0.115
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=47.4)
A:
NA
C2:
PF0004624=Homeobox=FE(43.9=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:
AGTGACGATGAAGACAGTGTCTG
R:
CTTTGCTCTCTGGTTCTGGAAC
Band lengths:
243-347
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]