GgaINT1016697 @ galGal4
Intron Retention
Gene
ENSGALG00000001735 | LHX4
Description
LIM homeobox 4 [Source:HGNC Symbol;Acc:HGNC:21734]
Coordinates
chr8:5959958-5961369:-
Coord C1 exon
chr8:5961215-5961369
Coord A exon
chr8:5960130-5961214
Coord C2 exon
chr8:5959958-5960129
Length
1085 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GTCCCCATCGCCCGCTCCAGGTG
3' ss Score
6.93
Exon sequences
Seq C1 exon
ATGACTCCGAGGCGGGGGCTAAGCGGCCCCGCACCACCATCACAGCCAAGCAGCTGGAGACGCTGAAGAATGCCTACAAGAATTCCCCCAAGCCTGCACGGCATGTGCGGGAGCAGCTCTCCTCCGAGACGGGGCTGGACATGAGAGTGGTGCAG
Seq A exon
GTGAGACCAAGGGCAGGCCTCTGCCCACAGCCCAGCACCAGGCTGGGCCCCAGCGAGGGCTTGGGTTGGGTTCCAGGTGCTGGGGTGCAGGGGTGCCGTGGTGATGTGATGCTGGATTGTAGGGGTGCAGGGATGCTTGGTTGCAGGGTGCGTGGAAGCTGGGATGCAGGGTGCTGGGGTTCCTGCTGTGTGCAGGTGCAAGGTTGCAGCATTGCTGTCGTGCTGGGCTGCAGAGGGGTTAAACTGCATGGATGCCAGCGTGCTGGGTAGTCAGGTTGCAGGACTGCTGGCACGCACGTTTGCATGCGTGGTAGGCTGCATCAGTGCTGTGCTGCCATGGTAATGAGGTGCAGGTGTGCTGGATTACATGGATGCTGGGTGCCAGGGGTGCTGGGTTACATGGATGCTGGGGTGCTGGGTTGCAGGGTCACTCATTTACATGGTGCTTGGTTGCTGGGATGCTGGGATGCAGAACTGTGGGGATCCTGGTGTGTCGGGGTGAAGGGTTGAAGCAGTGATGTACTGATTTGCAGGGCTGTTGCACTGTATGGGTGGTAGGCTGCATGAGTGCTGTCATGCCATGGTAATGTGGTGCAGAGATGCTAGATTGCATGGGAGCTGGCATACTGGAGTATGCTGGGTTGCCAGGGGTGCTGGGCTGCATGGATGCTGGCTTGCTGGGGCATTGAATTGCAGGGATACTCAGATGCGCAGCGCCTGGAAGCTGAGGTGCTCAGGTGCTGGCATGATAGGATGTGGAGTTGCTGCAGGGATTCTGATGTGCAGGGGTGCTGGTTTGCAGGGGTGCTGGGTTATATGGGGGCTGGGGTGCTGGCGTGCCATGGTAATGGGGTGCAGGATTGCACAAGTGCCGGCATACTTGGTTGGATTGCTTGGTTACACAGCTGCCTGGAAGCTGTAGTGTCGGGTTGTGTGGGTCCCATTGTGCGGGGACGCAGGGTTGGAGCAGTGATGGATGCTGAATTGTATGGGTGCCAGATGGTGTGGCTGGGAGGTGCTGGCACGCAGGGCGCCGGGATGCCGGGTTGCAGGGCCGCCACCGACGTCCCCATCGCCCGCTCCAG
Seq C2 exon
GTGTGGTTCCAGAACCGTCGGGCCAAGGAGAAGCGGCTGAAGAAGGACGCGGGACGGCACCGCTGGGGCCAGTTCTACAAGAGCGTCAAACGGAGCCGCGGGGCCGGCAAGCTGGAGAAGGAGAGCTCAGCTGAAGACTGCGGGGTCAGCGACAGCGAGCTCAGCTTCCGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001735:ENSGALT00000035845:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.654 A=NA C2=0.379
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(77.2=84.6)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=19.0)
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:
GCACCACCATCACAGCCAAG
R:
GGAAGCTGAGCTCGCTGTC
Band lengths:
294-1379
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]