GgaINT1016694 @ galGal4
Intron Retention
Gene
ENSGALG00000001735 | LHX4
Description
LIM homeobox 4 [Source:HGNC Symbol;Acc:HGNC:21734]
Coordinates
chr8:5963134-5966580:-
Coord C1 exon
chr8:5966416-5966580
Coord A exon
chr8:5963306-5966415
Coord C2 exon
chr8:5963134-5963305
Length
3110 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
CCGTTCGTCCATCCCCGCAGAGA
3' ss Score
10.55
Exon sequences
Seq C1 exon
CGCACACGGGAAAAAGAGAGTCCCGTAAATAGACTTTCCGTAATCCTGTTCGGTGCCGGCCCGACGCTCGCGGAAGGGGCAGCGCTGGGGACCCCCCCCCGACACCGATGGGCACCCGATGTGGCCGCTGCGGTGGGGCAGCACCGCGGTGTGCAGTGCTCACAG
Seq A exon
GTGGGCTGAAATGGGGAGGGAGGGGGGGGGAGCCGTGCTGCATCTCCCCCCGGGGCCGCCCCTTCCCATCGCCGGTAATTACCCAAATGGCGCAGGCTGATGGGAGACAGTCGCTATTCCCTAATAGAATTTGCCCTCAAGTGCAATTTAATTTTCCTGGGCCAGCCGCCCCCCTCGGCTCGCTGCCGCCCGCTGCTCCCTTTCTCCCCTCTTTCCTTTCCCTCCTCGATGCAGGCAGGAGCGTCTCTCCGGCCATAAAATCGCGGGGTTGGGGGGTGGGGGGAACCCTTCATGTCTGCTCATTCCCAATTAAAATTAACAGCGCCCTGCTTGGCACTCCCTGCGTTCTCCAGCCGCCGGTAAGTGCCCGCTCTGCGATTTCTCCATGCGATGGGGGTGGGGGGTGGGATGCGGGGGTCCGGATATCCCCGTCCCAGTTGGGGCGGCGTGGAGAGGATGGGATTCTCCAACCCTGACGCCCTCTCAGGGCACCGGGAGGAACGAACCCTAAAGCCATCCGAAGGGCAGCACCGCCGGGAATAGATGGGCGAGGGAAGGCGCGGGAGGGGACGGAGTGGGGCGAGGATAGGGGTGGTGCGGGGAAGGTGCTGCGGGGGTCAGGGGGAGCCCCTTTGGCCGCGTTCTGCAGGGATGGGGCGATGCGGATGGCGGTACGGGGGGGTCCGTACCGACGTGCGGAGCAGAAAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGGGAAACCGTGCGGTGGCAAATAGGGGCATCAGTGCGGGGCCTCCGGCCGGGATCCGGAGAGAGGGAGAGGGGCTGCAGCCCCCCCCCAGGGGTAGCTCTATCATTATTAGAGTATTTCATTCTTTTATTTTGGCCTCCCCCCTCCCCATCCCCAACACGGCTCACAGCGATGGGTGCCCTTTGCCGTTCGCGTTTCCGATCGCTGGCAGATCTCATTTCTCCCCCCCCCCCGGCCCCGCACAGCGCCTTTCTGCCTTAACCCCGACGTTCTGCATCGACTTCAGCTCAGCGTTGGGGAGCCGAGAGCTGCGGGGTGGGCCTATAAACCGCCCCCCCCCTCCGCTACGGCCAGCGCTAATTGACACCCTCATTAAGAACTCTATTTCCTTTAGGGGCAGGTGGGCAAACGTGCGGCAAACCTTTGTGCCGAACCCAAACTTCTGCCCAAAGCGCCTTCCCAAAATAATAGTAATAATAATAATAACAACAATAATAAACGAATACATGGACGGAACGACCATTAAAATAATAATAAAAAGAAGAAATAAGAGAGAAATCGATCTCTGTCGATGGAATAAAACCAACGGGCTGTGCTGCCAACTCGCAGTGCAGTGGGGGGGGATGGGGCACGATCGGATCCCTGCATGTTTATATATATATATATGTGTATATATATATATACACACATAAATATATGTGTGTGTGTATATGTGTGTGTATACATGTATATACATATGTGTGTGTATATATGTGTGTATGCATGCATATATGTGTATATATACGTGTGTATATCTATGTATACGCAGATGTTTCTCTCTCTCTCTCTCCATCTATATATCAGATCAAATGAAATTATCCGAGCTATTTTAAAATAAACGTAGATGCGCCGTTATCTGAAGAGCTATTTGTTAATGTACCCATCGATTTCTGGGGCTGTGTGGGGCAGATGGGGCGCTGCACACCGCGGGTGGTTCCGTTCCCGACACGCGTTCCCGCATCGCTGTGCCGGACGCGCTCCGTGCCCCCCCCCCGACCCCCCCGCAGCCGTCCGTAGGGATAACGAAGGGGGTTCTGTCGCTCCGCGTTGCCGTGGGGGCGTCCCGCGGGATCGGCGGCGTCTCCGCGCGGTGCTGTTTGTTGATGCCCCCCCCCCGGGCTCGGGGTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTTTCCCCCTTTTATTTCTCTTTCCTTTCCCCTTCCTCTTCCATTTTAATTTCTTGTATTCCTTTTATTTTCTTTTCCTCCATACATCCATTTCCCTTTTTCCCTTTTCCGTTTTCGTTTCCTTTTTTCCTTTTTCCTTTTTTTTTACGTTTTCTTTCCTTTATTTTCTCTTTTATTTTTTCCTCTTCTCTCTCCTTTCCTTTCCTTTCTCCCGTTCCTTATTCCCTTCTCTTTATTTCGTTCATTTCCTTTTCCTTCCTTCTTCCCTTTCCCTTTTTATTTCCCGTTCTTTTTCTCTTTTTTCTCTCTTCTTTTTTCTTATTCTTTCTGCCTTCTTTTTTCTTTCTCCCCTCCTTTTTTTTTTTCTCTCTGTCTTCCTTCTCTTTTCGTTTACTTTTTTCCTCCCTTTAACGGATTTGCATTTTCTTTTTCCATCTTCTCATTTCCTTTCTTTTCCCCCTTTCTTTTCCTTTTCTCTTTTCCTTTCCTTTCCCCCCCCATTTCTTTTCTTTTTCTCCGTTCCTTTCTTTTTTTTCCATTTTATTTTCTTTTCCTCTTTTCCTTTTCTTCCCCTTTTCTTTTCTCATTTCCTTTCTTTTTCCCCTTTCTTTTCTTTTTCTCTTTCTTTTTTTTCCCATTTTATTTTCTTTCCCCCTTCTCTTTTCCTTTCTTCTCCCTTCTCTTTCTCCCTTCATTTTTCCTCCCTTCCCTTTCCCTTTTTCCCTTTCCGCCTTCCCCCTTCCCCCTTTTCTTTCCATTTTCCATTCCCATTTTCCTTCCCCTTTTCCTTTTTTCCCCCTTTCATCCTTCTCGTTAACCTTTCCCCTTCCCCTCCTCTTTTCCTTCCCTTTTCCTTTTTTCCAACCTCTTCTCCCTCCACCACCCTTCTTCCCCTCCCCGTTCCCCTCTCTCCCCCCACTTCCCCTATCCCCGGCTCTCCATCGGGGAGCGCGAAGCGACGCGCGGTGCCGCCGGCGCTGAGGCCGCTCTCCCGTTCGTCCATCCCCGCAG
Seq C2 exon
AGATCCCCCAGTGCGCCGGCTGCAGCCAGCACATCCTGGACAAGTTCATCCTGAAGGTGCTGGACCGCCACTGGCACAGCTCGTGCCTAAAGTGCGCCGACTGCCAGATGCAGCTGGCCGAGCGCTGCTTCGCCCGCGCCGGCAGCGTCTACTGCAAGGAGGACTTCTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001735:ENSGALT00000035845:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=91.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]