GgaINT0124505 @ galGal4
Intron Retention
Gene
ENSGALG00000001347 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:HGNC:21735]
Coordinates
chr17:8725794-8728094:-
Coord C1 exon
chr17:8727874-8728094
Coord A exon
chr17:8725895-8727873
Coord C2 exon
chr17:8725794-8725894
Length
1979 bp
Sequences
Splice sites
5' ss Seq
ATGGTACGT
5' ss Score
9.89
3' ss Seq
ACTGGGCTTTTCTTTCACAGGCA
3' ss Score
10.65
Exon sequences
Seq C1 exon
CCGCTTCGGTACCAAATGTGCCCGCTGCGGCCGGCAGATCTACGCCAGTGATTGGGTGCGGCGGGCGCGCGGCAATGCCTACCACCTGGCCTGCTTTGCCTGCTTCTCCTGCAAGAGGCAGCTCTCCACGGGCGAGGAGTTCGGCTTGGTGGAGGAAAAGGTGCTGTGCCGGATCCACTACGACACCATGATAGAGAACCTCAAGCGGGCAGCAGAAAATG
Seq A exon
GTACGTGGCCACGACACAGCCCTTGGCCCAGGTACTGTGTGGGGGATATCGCTGCACATGGTGAGGGGCCAGGGCTGTTTCCATGCATGGAGAGTAGGATGGTGCCTGCAGAGCAGCTGCTCCTGCACTGGGCATGCACGGGTCCTGCGGCAGAGCCGTGTGCTGAGGGCAGTGCTGAGCATGGCCCCAGCCCTGCTTCCACCGCACCGCTGTGCCTCGGTGCCGCATGTGGCAGGTCAGAAAGCCGTGGGGATTTGGAGGCTGTGAGTCATAAATCTAGAAGGTGGGAAACCTGGCGGGTGGACAAACCCTTCCCATCATTTTCCACTGGCTCTGCCCACCCAGGGATGTGCTGCAAGTGGCCTTCATGTTTCCAAATGTATCCCACTGCTGCCGGTGCCATGAGGTCATGCAGTGTCATGGCTGCGGGGCAGCGGCTGAGTGGGTGCTCAGAACAAAGTGGCTTTGGAGGGTTTGTGAGGCCATGCCATATCACATTATCACTGGGCTGGGCCAGGGAGGAACCGGCCCCACATTCTCAGGCTGTGGCTGGCTGTGTGGCAAGGCGTGGAGTAGAGCTGCAGAGGGCCTGCCTGCTTCTCTGGTGCTCAGCTGGATTACAGGGACACTGCCACCGAGATACTGTGCAGCTGCGGAACTGCCAAGGGAAGTGCCTAGGGACCCTCTGGCACTGGGAGTGCAGCTCCTGCCTGTGTGCCACTCAGTAGTGCTTCACGGGTGTGGGGAGGCCAATGCCACGTCCCAGCCTGTGCAGCATGTGGAAGCGATTAACAACCTGACATGAAAATAATCAGTGTTTCTGTTTACAGCATTTGGGTAAGAGGATGGAAACTGTGTGCCCTGTTGGGCTGGGAGGCTCCAGTGGCTGGCTGGTGTGAAGGGCACAGCGCATGCATGGAGGGGCTGTGGGTCTGGGGGAAGCATGGGGCTGTCGGGCTGCAGCTGTGGCTGGATCTGTCTGCAGGATCCTGCAGTGCCCCGGTCCTGCCCAAGGGCTGGGGTTTGTGTTGCAGAAGTGGCCGTGGTGGTGCCAGGACAGGGGCTGAGTGTCCCCAGGCAGGTGCCCACCTCCCTGTACCCCTTGGCTGGAGGAGGGGATGGGAAGGCTCTGGGGAGCAGTGCTGCTGCAGAGTTAAAGGGCCACGCGTTTTTCCCTCTCCAGTAATTACCCAGCAATTTCTTCTGCACATGAGGTTTTACACACAAGAAAAATAAACAGATGTTGCTGAAGTCAGAGTCCCATTCATCATCCTAAAAGAACAAGTCAAACTATATGAGAAAGTCCTTCAACTCCAGCCAAGACAATCACAGCCCTGTCCAGCTTGCAGAGCAAACACCGTGGTGTGCAGGCGCATCCTGGGAGCGGGGCGAGCGCCAGCCCCGTGCGTGCACCCTCTCTCATCCATCACTTCTCTGGGCAGTGCATGGGCTCCACTGCGGACCCCAGTGTGGGGTGGGGGCCCTGGCCCTGGCCCTGGCTTTGGCCTCTCCCGCAGTGGCTCCATGGCTGTGTGAGCACAGCCAGGCTTGCCTCAGCACCTCTCCCTGCAGAACGGCTGCTGCCCTGGGCAGTGGTACCATGCAGACTGGTGCCGTAGGGAAGGGGTTGCTTCTGTTGTTACTGCCTCAGGGCCCAGGAGGAGGTCAGGGAAATTTGGGGCCAGGGAAAAGAGTAAGGAGCCTGTTGAAATGAGGCAGGTGATGGAGACAATGGGGATGAGGCATGGTGTGGGTCCTGGTGTGCCCAGCAGCAGGCAGGGCTCCTCTGGGCTGCTTTCTGGGGGATGCAGCCAAGTGGTGACCATGAGCCGGGGCTGGCAGGATGTCAGTGCTTTCCTTTACTGACCTCAGAATCCATCTTCCCACTGCCCTTTCCCCATCCATAATTCCCCACATCTTCCACAACATTGCTGCTTTTCTGCTCCTTGCTCTGACCTCACTGGGCTTTTCTTTCACAG
Seq C2 exon
GCAATGGGATCACACTGGAGGGGGCCGTGCCCTCAGAGCAGGACAGCCAGCCAAAGCCAGCCAAAAGGGCCCGCACCTCCTTCACCGCTGAGCAGCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001347:ENSGALT00000002057:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.824
Domain overlap (PFAM):
C1:
PF0041217=LIM=WD(100=77.3)
A:
NA
C2:
PF0004624=Homeobox=PU(21.1=35.3)
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:
CTTCGGTACCAAATGTGCCCG
R:
CTGCTCAGCGGTGAAGGAG
Band lengths:
313-2292
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]