GgaINT0036060 @ galGal4
Intron Retention
Gene
ENSGALG00000003424 | LMX1A
Description
LIM homeobox transcription factor 1-alpha [Source:RefSeq peptide;Acc:NP_001244317]
Coordinates
chr8:5163547-5163772:+
Coord C1 exon
chr8:5163547-5163624
Coord A exon
chr8:5163625-5163702
Coord C2 exon
chr8:5163703-5163772
Length
78 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
TTCCCCTTCTTTTCACCCAGATG
3' ss Score
9.92
Exon sequences
Seq C1 exon
GTGCGGGAGACACTGGCAGCCGAGACAGGGCTGAGCGTGCGCGTGGTGCAGGTCTGGTTCCAGAACCAGAGAGCAAAG
Seq A exon
GTGGGTGCAGGGGCCCCCTCCTGTCCTCTCCTGCAGCCGTGTCATGACCCCTGGCTCTTTCCCCTTCTTTTCACCCAG
Seq C2 exon
ATGAAGAAGCTGGCCAGGAGGCAGCAGCAGCAGCAGCAGGACCAGCAGAACACGCAGCGCTTGAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003424:ENSGALT00000005411:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.115 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(43.9=100)
A:
NA
C2:
PF0004624=Homeobox=PD(3.5=8.3)
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:
GTGCGGGAGACACTGGCA
R:
CTCAAGCGCTGCGTGTTCT
Band lengths:
143-221
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]