HsaINT0091723 @ hg19
Intron Retention
Gene
ENSG00000107187 | LHX3
Description
LIM homeobox 3 [Source:HGNC Symbol;Acc:6595]
Coordinates
chr9:139088096-139090666:-
Coord C1 exon
chr9:139090498-139090666
Coord A exon
chr9:139089590-139090497
Coord C2 exon
chr9:139088096-139089589
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
ATGAGCCTTCCTTGGCGGAAATGGGCCCGGCCAATGGCCTCTACGGGAGCTTGGGGGAACCCACCCAGGCCTTGGGCCGGCCCTCGGGAGCCCTGGGCAACTTCTCCCTGGAGCATGGAGGCCTGGCAGGCCCAGAGCAGTACCGAGAGCTGCGTCCCGGCAGCCCCTACGGTGTCCCCCCATCCCCCGCCGCCCCGCAGAGCCTCCCTGGCCCCCAGCCCCTCCTCTCCAGCCTGGTGTACCCAGACACCAGCTTGGGCCTTGTGCCCTCGGGAGCCCCCGGCGGGCCCCCACCCATGAGGGTGCTGGCAGGGAACGGACCCAGTTCTGACCTATCCACGGGGAGCAGCGGGGGTTACCCCGACTTCCCTGCCAGCCCCGCCTCCTGGCTGGATGAGGTAGACCACGCTCAGTTCTGACCCAGGCCCGGCTCCACCCTGCACCTCACACGAGGGAGCTGCCCCTGGGTGGGCGGCTCGGGGCTGCTGGGGTTTCCGAGGAAGTGGGGCCAGGGCGTCAAGGGAGGGCTGGTGCCTTCGGAGCCTCCCACTGCCGACCGCACAGCTCCCTCTCTGGGGGCTGAGGGACCCACCTGGCCCCTCCTCTGACACAGGGCTGGCCCGCCAGGTGGCCTCCCAGCAAGCCAGCCTTTTTTGTAAGCAAATTTCTCCCCTTTATTGACCAATTAACTGAGCACTTGCTGCTATTTCTAGACATGAAATGTCACCTTGCTGAGGCCCAGCCCAGCCCAGCATAGCCCGAGGGCTGGAAAAACGCTTTCATCTCTAAAACTGAGAAATCATCATAATTGTGCTTTCACTTCCCAGGCTCCATGTGTCTTGGAGCCGTCACCCCGAGGCTCCCTCTTTAGGTCGGAGATTGGCCTTGCCTGTCGAGGCAAGAGGCTGCAGAGGCGGGGACACACCTGTGTCCTCCGGGAGAGGCCCCCTCCTCTCCCCAGACCACAGGGGGCCTCTCTGCCTCCAGCCCCACCTTCCCCGGGAGAAGCTTTCCCCAATCCCCAGGTCTCTAGATCATTCTGTTCTCGAGTATCCTGTGGAGGAGGCAAAAATGCCTGGCGCCCCTTCTCTCCAAGCTCAATTCTCTAAGCCCCTCAGGGTCTCCTCCTCACCCCACCCCAGGCCCTTGGTGTCCAGGCTGCACCCACAGATGTCTGTTGCCAAACAGCCTGCCCTCCCTGCCGGAGCCGGCTCTGCCAGCCCCAGATTGGGAAGTCTCCCCGCTGGAGAAGGGTGGGGCTCCTCTGAGCCTGCCCTGCCTCCTCCATCAGATCCTTTGGGAAGAAGTTTCTGGGAGATGCCCGCAGCTGTGCGTGCCCCAGACACAAAGGCTGGCCTGTGTGTAAGTCAAAGTCACTCCCGCAAACCTGAATCTCGAGCTACCTATTGGTTCTGTGAATGTTCTGTGTCTTTTATTTATTCTCGGGTGATCAGCTCTTTCCAAGACTTCAATAAATTTGTCAGTTACAGTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107187-LHX3:NM_014564:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.754 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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)