GgaINT1016698 @ galGal4
Intron Retention
Gene
ENSGALG00000001735 | LHX4
Description
LIM homeobox 4 [Source:HGNC Symbol;Acc:HGNC:21734]
Coordinates
chr8:5958429-5960129:-
Coord C1 exon
chr8:5959958-5960129
Coord A exon
chr8:5959868-5959957
Coord C2 exon
chr8:5958429-5959867
Length
90 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGC
5' ss Score
8.02
3' ss Seq
TCCGCTCCTTGTCCCAGCAGACG
3' ss Score
8.65
Exon sequences
Seq C1 exon
GTGTGGTTCCAGAACCGTCGGGCCAAGGAGAAGCGGCTGAAGAAGGACGCGGGACGGCACCGCTGGGGCCAGTTCTACAAGAGCGTCAAACGGAGCCGCGGGGCCGGCAAGCTGGAGAAGGAGAGCTCAGCTGAAGACTGCGGGGTCAGCGACAGCGAGCTCAGCTTCCGCG
Seq A exon
GTGAGCGGGGTAAGGGGGTGCGGGGCGGGGGTCCGCGGGGCTCCACGTGCACGGCTGACACCCCACGCGCTCCGCTCCTTGTCCCAGCAG
Seq C2 exon
ACGACCAGATCCTCTCCGAGCTCGGCCACACCAACCGGGTTTACGGCAGCGTTGGCGACGTGGCAGGAGGACAGTTGCTGAACGGTGGCTTCGCCATGGACGGGACGGGGCAGCCGTACCAGGACTTGCGGGACGGCAGCCCCTACGGGCTCCCCCAGTCGCCGTCGTCCATCTCTTCGCTGCCGTCCCACCCGCCCTTGCTCAACGGGTTGGACTACGCCATGGACAGCAGCATGGGGCTGGGGGCGCAGGGGGTGAGTCAGACGCTGCGCGCCATGGCCGGGGGGGGCCCCACCTCCGACATCTCCACGGGGAGCAGCGTCGGGTACCCAGACTTTCCCACCAGCCCGGCCTCCTGGCTGGACGACATGGATCACCCCCCTTTCTAAGCGCTGCTCGCCCCCGCCCCGGCCCCCTGCGTGCTCCCCCAGCCCGCAAGCGCAGCGCCGGAGATGCGAGATGGTGCCGGGATTTGCCGTGGGAAGAGGAGCCGGAGGGATCCGTGGGGGCTCGGCGCCCATCCTTGGGGCATCGGTGACGTCCGGGGCTCGGGATGGGGCGGGTGCCTTTGGGTGTAAGCACAAGGGAGGTGCGGGCGCACAGCACGGCGAGGACGTCGGGGTCACCCCGCCTTGTCCCTCCTGGTCGGCGGAGAGCCGCGCGTGCAGGAGGGGAGGACAATCAGGGATGGCAAAGCCTTTGTGGCAGAAGGGTTCGTTTCAGAGCGTTTCTCCCGGCCCGGGGGCCGTGCTGGCTGCTGGCTGCAGCGCTGGGCGGGTGGGAGCGGGGCTGTCGCGCTGCGGCTGCAGGGCCGTGATTTATCCCCGGGCGTGCAGGAGTGCTTACGGTGCAGCGCTGCACCTCGCTGGCTGGCGGGGAGGGATTGCAGCAGGAAGAAAAGCCTCGAGGCTGAGAGAGCGAGGGCACGGCCAAGCTGGGGCTGGGACGCGGGGAACGACGGTGGGGAGCGTGGGGTGAGCCTCCGCCGCTGGGTATTGCAAAAACATTCCCCAGAATGGTGGGGGAAAAGGGTCCGTGCTCGGGGATGCGCGTGGTCGGTGGCGTTCGGTGACATCAGGCTGTGCTGGCTGCTGCCCGGGCCGAAAGCGAAGGGAATTACGAGGAAACGCGACATCGAGTGAGAAAGCATATGGGCAGGCTGTCCCCTGCCTGGGTGCGTTGGTGCTGCAGGACTGCCCAGCTGCACCTGTGTGCCCCCAGCCGTGCCCCCCCTTCCCCCCCCCGGTGCTGCTCTGTGCCAAGCCCCCAGCCCCTGGGTGGCACAGGGAGGGGGCACGGAGGGGGAGGGGAGGGGATGTCCCTGCAGCAGTCCCTGCTTGCTCACCATCCCCATCCGATGCAGCCAAACGTCCTCCCCTCCCCTTGTAAATGTTGTACAGTTCCAGAAAGTGAGAGTCTTGTTTGCTGAGAAGGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001735:ENSGALT00000035845:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.379 A=NA C2=0.682
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=19.0)
A:
NA
C2:
NO
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:
TACAAGAGCGTCAAACGGAGC
R:
CGTTCAGCAACTGTCCTCCTG
Band lengths:
181-271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]