GgaINT0038979 @ galGal4
Intron Retention
Gene
ENSGALG00000011369 | LHX8
Description
LIM/homeobox protein Lhx8 [Source:RefSeq peptide;Acc:NP_001035556]
Coordinates
chr8:28613140-28616147:+
Coord C1 exon
chr8:28613140-28613243
Coord A exon
chr8:28613244-28616051
Coord C2 exon
chr8:28616052-28616147
Length
2808 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAG
5' ss Score
7.1
3' ss Seq
TTCAACTCTTATCTTTTCAGGTT
3' ss Score
11.4
Exon sequences
Seq C1 exon
GTAATGGGGTTAGTATGGAAGGAGCACTGTTAACAGAGCAAGATGTTAATCATCCAAAACCTGCGAAAAGAGCTCGGACCAGCTTCACAGCAGATCAACTCCAG
Seq A exon
GTAGAGGCAACGCTAAAACGCTTGAGTATTTCAGGTTTATGCAGGATGTAACTTCTGAACTGATAGGAAATCAGATGCATATGTGGGGGAAGAATAAGCTTGTATGCTTTATACTTTTTCAAAAACTATCAAGACATGGCATGTTTCTGGAATAGTTTGTGAGCTTCAGTGGTTTCATATGAAATAGTTACCCTTCGAGCTTTTTATTTCCCTGGGGGCAGCCAGTAATTCTGCAGAGTGGAAACAAAAAGCTTGATCTATTTTGATTGCTTGATGAAATCTATTTAAACAGACGTTTACATCACTGCACATAATAAAGAATATTTTTAGAGTTACGTAATATGAAGAGTTGTACTAGATATGGGTACTGGATATGACTTCAAGACATTAACAGGCAGGAAGCTTCAGTTTTATTGCAGTGCTCAGTAAAGGACTGCAAAAGTTTGTGTTCTCAGGACAACAGGTAAGTGTCGTGGACTCCTGTTAATCATCATGTGAATACAGCTCAACTCCTGTCAGTAAATGTTTTGTTTCTTTTTGTTTTATAGAGAGCAAGGGGAATAATTGCGTGTTTTTTTCATCATAATTTTTCTCCATACTTGCTTTTTAGATAATGTCTTGGCTATATTGATGTGCACTGGAAAGGATAGACTCTTAGTAGGGACTCATCTTTGCTCTCCTTCCCTCTTTTCTTTCCCTTCTCTTAGCCCTTCCAAAATGCTTCACAAGCATGCTCAATCTCAAGTATCTTTGAGTTTTGCTGCTGCCTGTTTAAACAAACTGAATTCTGTAGATTTGGTGTCATGTTTCAAGAGCCTAGCTTCAGTATGTAACGCTGCATGTTTGAGAGTGGGGGGGCAGACAGCTTTTTCATAGAGCTGGGTGGAGTGAAATAGAGAAGTGCATTTGAAGTTCTTGGCAGCAGTTTTTTTTACTGTCCAATTTGTTCTTGATCATGCATTATCAAAACATGTTTTTTCAATATCCTGTTATACGAGCTCAACCACTAGTTGAATTCTTTTCCAGTGTCAGGACAAAAGGGAAGTGGGAGCCTTGGAAGTCTGGAATTATGAAATCAAAACTCCTGGTAGGGTCATGCCTGCCTGGTGGGGGTGGGAACTGCCTGCATCTGCTTTGCTCTCAGAGCTTCTCATCTTGGTGCTGTCTTGACGAGAGTTGACTCTGGATTGCCTCAAATATGAGTAATTTCTGCCTCTGGATCACCACTTCACCAAATCAGCCTGTTAGGGAAAAACACCATGATCAGTGCCAGCTCACTGTGAGGAGGGTAACAGCAAGACCAGATTCAGAAGAGTCAGCCTGTAGTGGAAAGGAAATGGCAGCTTTCTCCCTAGTTCTAGCTATGCATCTTTCATGTTAATTAATATTTCTTTGGATGCATACTGCCACTGCAGTGTTCATTTTCTTCTGTCCTGCTTTGTCACCATGTCCTTCTCTTGTCTGTGGAAAAAGCAGTCAAGTTTAGTTAAGCTGAGGTGTGATAATCAGTGCATAACATGGCACACATTTGTATGATGCTTGATTTGCTGTTTGATCCATGACTGAAGTCAGGGTGTTACTAATCTAGAACAAGAGCACAACCTGGGTGGGGCCTAAGGTGCAAAGGCTCTGGGCATCAGGTGTGAATTTCTGCAGGAAGGAGACTTTCTTTTCTGACACGAGCTGAATGAATGACAGGTCCAGCTTTCAGAGTAGGAACTGAATTCAGGGCTTCTTCTGTTTTGACGTCAATGAAACTTCCATGTTTGCTTTTCCCGTTTTACTGGATTGTAACCTACTTCAGCAGATGTGAGATTTTCTTTTCAGACGCTTGCTGTCTGCTCAGTGCATCTGTCTCGGCACCTGTTCTTGATGTGAGACTTCCAGTAGTGTGCCTAAGGATGCAGAAGGATGTCCATGTTTTTGATGTTCTTGCATGAAACTCAGCAGGAAAGTAAATAGTTTAAACATTTTGGACTTTGAAGAGTAGTTGACTGAGTTCCTCAAAGATGAAGCAAGGCAAAATTTGCAGACCTTCAAGGAACGAAATCCAGAAATGAGAAACTACAGTTTACTAAATTGCTGAAGAAGTCCTGCAGAAATCTGTGAAGTCTTACTTCTTAATTAAGGTAAAATCTTACATGCTCCAGAGCTGTTCAGGATGCGGGTCAGGTTGACATCTACTTCCTCAAGAACTGTAATTCAGGTGATAATGTGATTGTTTGTAACAAAAGATGAGTCCAGTCAAATGGCTGCATAGTGCAGGTCTGTCAGTGTGCAGCCTGAGAGCCTCTCACATCAGTGGAAAGTAAACGTGGTATAAGACCACATTCTCCACGTAGCTGAAAAGAACATCAAGTTGCTCTGTATAGTGCAAGATGCAGATAGCAATTGACAAGCTCAAAGAACCCAACCAAAGCTCATTCCTTCCTTATGCTGTTTGCTGTGGTCTGTTGCTGTAAACATCTTCTTTATCAAGTATGCTTGAATGGCTTCACAGTGCGTTTTCTTCCACAGTCTCTTTAGTACAATCATAACTGAATGCTTTGTCCATTTCTGACCGATTCCAAGCATAATTCATTTGTCATAAAAGTTCAGTTAAGCAGTATAAGGAGCTCCTATTTTGGGTGTGAATTTTGTGGATTATTTAAAATATATTTTTCTCCCTTTTACTGGGGACTGTCTGGGGACTGGAGATCACAACAGTTTCCTTTAAACAGAGAAGGAGAAGGACCATAGTCTGAGAGAAGTCTCTAATGCCACCCTTGGGACTGCACACACAAAAAAATTCAACTCTTATCTTTTCAG
Seq C2 exon
GTTATGCAAGCACAGTTTGCTCAGGACAACAATCCAGATGCACAAACGCTTCAGAAACTGGCAGAAAGAACAGGCCTGAGCAGGCGCGTTATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011369:ENSGALT00000018546:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.657 A=NA C2=0.500
Domain overlap (PFAM):
C1:
PF099434=DUF2175=FE(33.7=100),PF0004624=Homeobox=PU(21.1=34.3)
A:
NA
C2:
PF099434=DUF2175=PD(20.8=65.6),PF0004624=Homeobox=FE(54.4=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:
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]