GgaINT1016827 @ galGal4
Intron Retention
Gene
ENSGALG00000003424 | LMX1A
Description
LIM homeobox transcription factor 1-alpha [Source:RefSeq peptide;Acc:NP_001244317]
Coordinates
chr8:5160764-5163442:+
Coord C1 exon
chr8:5160764-5160996
Coord A exon
chr8:5160997-5163272
Coord C2 exon
chr8:5163273-5163442
Length
2276 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGG
5' ss Score
10.19
3' ss Seq
TGTCTGTACCCCATCCCCAGGTA
3' ss Score
9.6
Exon sequences
Seq C1 exon
GTTGTTCGCAGTGAAGTGCGCCGGGTGCCTGGAGAGCATCGCGCCCAGCGAGCTGGTGATGCGCGCCCAGCAGAGCGTCTACCACCTGCACTGCTTCTGCTGCTGCGTCTGCGAGCGGCGCCTGCAGAAGGGCGACGAGTTCGTGCTGAAGGAAGGGCAGCTGCTCTGTAAGGGCGACTACGAGAAGGAGCGTGAGCTGCTGAGCTTGGTGAGCCCGGCTCTGTCGGATTCCG
Seq A exon
GTAAGGGGCTGCCTGATGCAGCATTGCCCCAACCCGCTGCTCCTGCCCCAGGGTTGCTTGGCTGGGGGAAAAGTTCCAGTGCAGAACTGGGGTGGGATGCTGTAGGAATAGGGCAGGGGGTTGCATCCCTTGGAGCGGAACCAGTGGGAGGGATATTGAGATCAACCTTTAGACCTGAATGTGCAATTGATGCAACTCATGTCTGCGTGATACCCAGGATGACAAATTTAAGGAGAAACCCAACAAAATAGGAAATGAGCTGTGAGGAGAAAGTACTGGGTTAATGGTATCCCTGATAAAGGCATTGGTGCTTCCCAAATCACATAAAAAGATCACTGTAGGGAAATCTGCTTTGTGGAGGGAAGGATTTACCTTTGTGTGGGTGGGACAGGGGTGGGGATGAAGCAAGAATCACAACAGCTCTTTAATATCAAACTCACCCAACCTCCTCCCTCCTCCCCCTCCCCCCCCCAGAAAAAACCCTCCCCAAATAGCAGTGATGGTAACAAAAATTGAAGGAGGACAGCAAGGGTGGACCACTGTGCTGAAGCCCTGGGAAAGTGCTCTGGGGATGTCCTGATGGCTGTGGCACAGCGAGTTCTGCTCTATGGGGGACGCAAACGCCTTCGGTTAAAATAGGAACTGAGGAGGAAATGTCAGGCAGGAAAAGAACAGAATCAGCTGCTGATCCCACAACAGTTTGGGTTTGTTCCGACTGGGGGAAAAGGGCACTTTGGGAAAGGCTGGGGAGCTTTTCTCCCCCGTGGCTCATCAGCCCGTGGCCGGCCCTGCTCCCAGCTGCTGGCCAAGACGAGGGCTTTGCATTGCAGAAATTCCCCAGGAACACACTACTTTCAGTGGAAAAGTCCCAGCGGAGGGATGGAGGGGGACAATGTGGGGCTCACCAGTGCCACGCACCCCCTTGGATGGTGGGAGCCCATCCTGAGCTCCCAGCATCCCCAGGTCCCTCACCGAAGGATGCAGCCGTGTGTCCCCATGGGGCTGCCAGCCCCTCCAGCCCCCCCCATTCTCCACACAGCAAAGGCCACTTTATGAGAAAGTGAAGATAAAAAGCGAGCCATATGTTGCCCGTAATCTTCCCAACCCTCACTTCAATTACTGCCTCCTCTGAGCCCACCCCGGCCGAGCCTAAGCAAACAAAGCCCCTCTGAAAGAGGACCCCGGTTTCCAATTAAAAGCGTCCTAACTGTTCTCCTCTGCCTAAATCCTCCCAGGCGAGGAATGTCCCGGCCCTGCTGTGGCCACACTGGCTCCCCCCGTGCCGGCGAGTCAGGCTGGGGGCATGCACAATGTCCCCCACCCTGGCCCCTTCCCAGGTGACGTCAGGGGCAGCCCCAGACAGTCATTAATTTCCCCCCTCGTTGGGGAAAGGCTTGAAAGGGAGAGTTAATTAAAAGTAATACCCAGCCAAATCCGGCTCCGCTTCTCCTTTGACACATGGAGGGATTTGGGGAGCAGGTGCTGAGGGAATGGAAAGGGGGGTCGTGATCGGAGTGGGTTTTTCCCCTTCCCAGAGCATGGCAACGTGGGCCTGAGCACTGCGTGCTGAGCTCATCCCCTCCTAGACTAGGGACGGTGGGGCAGGCACCCCTCACTGGGGTGCAAAGGCATCTCAGTGTCTCTGTCAGTGCAGGTCTCAAATCCTAGAGTCTGTTAAACCTCTTCCCCTCCACCAAAAGTAAGCTCAGTGGTGGAAGCTCACATCCAGCTCCCCAAAAGCCACTGAAACACCTACTGGGAGCTGCTTGATTGGTGTGGCCATGGGCACAGCATCCCTCTTCCTGGGAACCACTGCTCCGGTCTCTCTGGGGACTACCAGTGCTGTGTTGCATGGGGAAGGTGTCCCAAGATGATGAGCAGAGCAGACATCCCACAAAGCAGGAGTGAGTGGGATTCATCCTCACACTGTGGGCATCAGACTTGCATATGGCCCATGCATCCCAGAGACACCGCAGTGCCACAGTGGGACTTGGGCCAGGCAACTCCTTGCAGCCTGCTGAGCACTGCATGGTTTCTAACAAGCAACTCAGCTTTGTTAGCAATTAACAAATAGTGAGCTTGCTGGAAAAGGCTGCAAGTGATTTACAGCTCATGAAGGGGAAGGACATGTTATGGCCAACCTGCATTGCACCTTGGTGCCAAGGACACCGGCACGGCGATGCCAGGGTGGGTGAAGATGAGGATGGCGCAGACATCCAGCCTCACAGAGGGACCTGAATCTTGGTCCCTTTTTGTTGTCTGTACCCCATCCCCAG
Seq C2 exon
GTAAAAGTGACGATGAAGACAGTGTCTGCAAAATGGGCCCAGCCTCAGCGAAGGGAGCTGAGGAGGGGAAGGACCACAAGCGGCCCAAGCGCCCGCGCACCATCCTGACCACGCAACAGCGCAGGGCCTTCAAGGCGTCCTTCGAGGTCTCCTCCAAGCCCTGCAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003424:ENSGALT00000005411:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.596
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.5),PF0041217=LIM=WD(100=74.7)
A:
NA
C2:
PF0004624=Homeobox=PU(47.4=47.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]