HsaINT0091723 @ hg38
Intron Retention
Gene
ENSG00000107187 | LHX3
Description
LIM homeobox 3 [Source:HGNC Symbol;Acc:HGNC:6595]
Coordinates
chr9:136196251-136198820:-
Coord C1 exon
chr9:136198652-136198820
Coord A exon
chr9:136197744-136198651
Coord C2 exon
chr9:136196251-136197743
Length
908 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGC
5' ss Score
7.85
3' ss Seq
AGCCTCTGCTTCTGTTGCAGATG
3' ss Score
9.83
Exon sequences
Seq C1 exon
GTTTGGTTCCAGAACCGCCGGGCCAAGGAGAAGAGGCTGAAGAAGGACGCCGGCCGGCAGCGCTGGGGGCAGTATTTCCGCAACATGAAGCGCTCCCGCGGCGGCTCCAAGTCGGACAAGGACAGCGTTCAGGAGGGGCAGGACAGCGACGCTGAGGTCTCCTTCCCCG
Seq A exon
GTAGGCGGAGGGATCGCGGAGCTCGGGGGGGGACGAGCGCGCGTCGGCGGGGTCGCAGGGGTCCCAGGGAGCCCGCGGATCTGAATTTCCCATGGAGTTAGTGGACTCCTTAAGTTCTACTTTCAAAAGCATTTCACTTACAGAACCTGCTCCCCCAGCACCCTCCCCGCCCTGGGTGGCCACTCCGGACCACTGCTTTTCCCCTGGTGGGGACACAATCCCTGTGGCCCGACCTGTCCCCAAGCTGGGCGCCTACGGGCTTTCTCATGGGGGGGTGGGCGTGTCCAGGCCGTCTCTCTGGCTCCTAGCCCTTGCAGTGATTTTTAGGAGAATGGGCAGTGCATTTCGGGAAAGACTGAGTCGAAGTCCCAGCTGCTTGGAGTTGGGGGAGGGGGCTACCTGGGGTCAGGGAGAGAAGGTTCCATACCCTTCTGTGGGGCCTGGATTATTTATTTCATTCTCCGGGCACCGGGGATGCTGCGTCCCCATCTGTTGATGCCCATCCTCAGAATGTGGACAAGACACTCTCTTTTGGGCTGCCTCGTGACCCGGGCTACTCACTCAGCCACTCTGGAACTAAATATCCTTGTCTGCAAAATGTGGGTGGTGGTATCTGTGCCCCCTTCCTAGGCTGCTGTGGGGCTGGTCCTGAAAGCCTGGGCCCTGGCTGGGCTGTTCCTGACTCTGATCCCACCAGGCCTGAGACACCTGGGCTGACTCAGGGGTGAGGGCAGTGGAGGGGCAGGGGCAGCCATGCTCCAACAGTAGAAGGGGCCTGTTATGACCTGTCATGTGGTGTGGGGCAGCCACTCTTTCTCCGACCCAGGGGTGCCTCCGCCTGCAGGATGGGACTCTGAGGGGCCGCAGGTGGAGGGCAGGCGCTGACTGAGCCTCTGCTTCTGTTGCAG
Seq C2 exon
ATGAGCCTTCCTTGGCGGAAATGGGCCCGGCCAATGGCCTCTACGGGAGCTTGGGGGAACCCACCCAGGCCTTGGGCCGGCCCTCGGGAGCCCTGGGCAACTTCTCCCTGGAGCATGGAGGCCTGGCAGGCCCAGAGCAGTACCGAGAGCTGCGTCCCGGCAGCCCCTACGGTGTCCCCCCATCCCCCGCCGCCCCGCAGAGCCTCCCTGGCCCCCAGCCCCTCCTCTCCAGCCTGGTGTACCCAGACACCAGCTTGGGCCTTGTGCCCTCGGGAGCCCCCGGCGGGCCCCCACCCATGAGGGTGCTGGCAGGGAACGGACCCAGTTCTGACCTATCCACGGGGAGCAGCGGGGGTTACCCCGACTTCCCTGCCAGCCCCGCCTCCTGGCTGGATGAGGTAGACCACGCTCAGTTCTGACCCAGGCCCGGCTCCACCCTGCACCTCACACGAGGGAGCTGCCCCTGGGTGGGCGGCTCGGGGCTGCTGGGGTTTCCGAGGAAGTGGGGCCAGGGCGTCAAGGGAGGGCTGGTGCCTTCGGAGCCTCCCACTGCCGACCGCACAGCTCCCTCTCTGGGGGCTGAGGGACCCACCTGGCCCCTCCTCTGACACAGGGCTGGCCCGCCAGGTGGCCTCCCAGCAAGCCAGCCTTTTTTGTAAGCAAATTTCTCCCCTTTATTGACCAATTAACTGAGCACTTGCTGCTATTTCTAGACATGAAATGTCACCTTGCTGAGGCCCAGCCCAGCCCAGCATAGCCCGAGGGCTGGAAAAACGCTTTCATCTCTAAAACTGAGAAATCATCATAATTGTGCTTTCACTTCCCAGGCTCCATGTGTCTTGGAGCCGTCACCCCGAGGCTCCCTCTTTAGGTCGGAGATTGGCCTTGCCTGTCGAGGCAAGAGGCTGCAGAGGCGGGGACACACCTGTGTCCTCCGGGAGAGGCCCCCTCCTCTCCCCAGACCACAGGGGGCCTCTCTGCCTCCAGCCCCACCTTCCCCGGGAGAAGCTTTCCCCAATCCCCAGGTCTCTAGATCATTCTGTTCTCGAGTATCCTGTGGAGGAGGCAAAAATGCCTGGCGCCCCTTCTCTCCAAGCTCAATTCTCTAAGCCCCTCAGGGTCTCCTCCTCACCCCACCCCAGGCCCTTGGTGTCCAGGCTGCACCCACAGATGTCTGTTGCCAAACAGCCTGCCCTCCCTGCCGGAGCCGGCTCTGCCAGCCCCAGATTGGGAAGTCTCCCCGCTGGAGAAGGGTGGGGCTCCTCTGAGCCTGCCCTGCCTCCTCCATCAGATCCTTTGGGAAGAAGTTTCTGGGAGATGCCCGCAGCTGTGCGTGCCCCAGACACAAAGGCTGGCCTGTGTGTAAGTCAAAGTCACTCCCGCAAACCTGAATCTCGAGCTACCTATTGGTTCTGTGAATGTTCTGTGTCTTTTATTTATTCTCGGGTGATCAGCTCTTTCCAAGACTTCAATAAATTTGTCAGTTACAGTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107187:ENST00000371748:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.772 A=NA C2=0.971
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=19.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGCAGTATTTCCGCAACAT
R:
GTACACCAGGCTGGAGAGGAG
Band lengths:
346-1254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development