DreINT0089064 @ danRer10
Intron Retention
Gene
ENSDARG00000039458 | lhx4
Description
LIM homeobox 4 [Source:ZFIN;Acc:ZDB-GENE-060728-1]
Coordinates
chr8:14420961-14423421:-
Coord C1 exon
chr8:14423267-14423421
Coord A exon
chr8:14421133-14423266
Coord C2 exon
chr8:14420961-14421132
Length
2134 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TGAGGCTTTTATGTCTACAGGTG
3' ss Score
8.83
Exon sequences
Seq C1 exon
ATGATTCAGAAACAGGAGCAAAACGTCCACGCACCACCATCACAGCCAAACAGCTGGAAACTCTCAAAAGCGCCTATAAGAACTCGCCAAAACCAGCAAGACACGTGCGAGAGCAACTTTCCTCAGAAACGGGCCTGGACATGAGAGTGGTGCAG
Seq A exon
GTAAGACTACAACTACATCAAACATAATATCCCACTCTAAACCACATGCCAAATTCCGGGATTTTTCACTGGCTAAAAAGCTGGACTTCTATAACTTATAATGAATAAATAACCGGCAGCTGTTGTTTCCTTCCAGAATTGTAGGATTCTGTGATCAACGAATTTAACGCAAAGTCATGGTGCAAAATTTAGAGGAGTTTAAAAATGTTTTAATTGCCGCAGATATGAATTGGCCGACAAGGACACTGTTCAAATTCCTTCTGTGCCATCTGCAATGTTTTATATTCAATAACATTATATTCACATGTAGAAAGTTCTCATTTGGTGTCTGACCCATTTTAGATGCATTATCATGCACATTCAGCAAAAACCTATTTGAATAAGACTACATTTGTTGCATCAATCGCTAAAATTGTCATTTGTATTATGATTTGTTTTATGTTGTTGTTGAGGAGATTTGAACCATCATATTTTCATCATTTAGAGTCATTCTTGTATCAAATATGAATCAAATATGCTTACACTGTAAAAAATGCCAGGTTCCACACAATCGATTTGGGTTAGGGCAACATGAAGGAGTTAAGTTAACATTAGTTTTTACAAATTTAAATGAATTGAACATAAAATAGTTCAGTTGCCCAAACCCCCCCCCCCCCCCCCCCCAACCAAAAAAGTGAAAAAAAAATCAAGAATTGTGTTGTTTCAACTCAATTTTAATAGATATTTTGAACAAACAGCAAATGCCATTTTTAAGTGTATGGTGAAGAGGTAAATCTTGGTTTCTATCAGTGCTTGATTTAAATAAATAACACAGACCAATGGTTCTTGAGGTCAAAAAACATAAGTGTAAAATGTGATGTGCATTCAACTTAAGCTCTTTAGACCATACGCCGGACGTTTCTCAGAGTTTCGCTGCAATGTCTTTAAAAAATATATTATTTAGGCCTATTTTCATTATTTATTTATTTTTCATTATTTGTTTATTATTATATACAATAATTGAGACATAAAATAAAATAGCAAACACTGAACATCTCTCTATATTTAGGCTTTATTTATTTATTTAGGCCTACTTATTTGTACTGAATGTTTCTGCTTTTATTTTAGTTGCCTTTTATTTCTTCAATTGTATTTCCAAAATGAATCCTCATTGAACTTAACAAGTTAACAATGATAATAACGTGTGTTAACAAATTTTTAATGATTGATATAGGAATTATAATGCTTTTTTATTGTTTTATCTTTATTTATAAGTAAAGTAGCATATTTACAGCTGGTGTAAAGACTATTTCTGTTCGTTCGCATCCTGTCCCTTTGTGGCCCCTGGCGGCATATTCACAAACTACGGTCATACATAAAAAAACACTTGCTTGCCCATTTAAAGCGGAGGCAGTATTTGCCTGGGCGGTAATGGCCACACTGAACTCTCACCTACTGTATGAGTGTATATAGCAAAACAAAACAAGAAATTTTGGCTTAATCATTGAGAGAATTTGCTTTTTATTTCATTTTATTTCAAGCCACAATAATTCAAAATTTTCTGTGATTTTTCCATGACTTTTCCTGAAACAGACCTTTTAAAAATACATGACATTTCAGAAATTCCATGACCTGTTGGTAGAGCTGCACGATACTGGAAAAAACTTACATTGCAATATTTTGACTTTCTGCAATTTATATTGTGATATTTTACAAGATAGCTTAATTAATTAACTTAATAATTTTAGACTGATTGTATTGATTTTGCATAAAATAACATAAAACAAATTAGGGAAAAAGTAGAGCAAATATACAAGTGAAGAAATCTAAAAGTATACAGGTAGAGAAATAAAATAATCAGTTGTACAATAGAGGCGTATATTCTTCATTGTGTAAATAATTAATACAATCAATCTTTGTTAAAGCTACAAACGCAAAAGTTCTTTGAGCTCAAATGCTTTTGACTCGCTTCAAATTTACACAAGCTTTAAAAACACAATTGAGAAACTTTTTACTTTATGCTAAACTGAAATGACTCCAAACTTCTATATGTGACTATTGCAGAACCACCCATCGCTATAGACGCTAAAGCAATATATTGTGCAGCCCTAGTTGATGTAAACTCTGATGTTTAATGAGGCTTTTATGTCTACAG
Seq C2 exon
GTGTGGTTTCAGAACAGACGGGCAAAAGAAAAACGGCTGAAGAAAGACGCGGGCCGGCATCGGTGGGGTCAGTTCTACAAAAGCGTCAAACGCAACAGAGGCTCCAGTAAAACAGAGAAGGAAAGCTCAGCCGACGATGCAGGACTCAGTGACAGTGAGCTCAGTTTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000039458:ENSDART00000057644:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.692 A=NA C2=0.552
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:
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]