HsaINT1018198 @ hg38
Intron Retention
Gene
ENSG00000107187 | LHX3
Description
LIM homeobox 3 [Source:HGNC Symbol;Acc:HGNC:6595]
Coordinates
chr9:136199678-136200753:-
Coord C1 exon
chr9:136200582-136200753
Coord A exon
chr9:136199881-136200581
Coord C2 exon
chr9:136199678-136199880
Length
701 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGC
5' ss Score
6.39
3' ss Seq
CGGCCCTGTGCGTCCCGCAGGCG
3' ss Score
9.64
Exon sequences
Seq C1 exon
AGATCCCGCTGTGCGCTGGCTGTGACCAGCACATCCTGGACCGCTTCATCCTCAAGGCTCTGGACCGCCACTGGCACAGCAAGTGTCTCAAGTGCAGCGACTGCCACACGCCACTGGCCGAGCGCTGCTTCAGCCGAGGGGAGAGCGTTTACTGCAAGGACGACTTTTTCAA
Seq A exon
GTGAGCCCCGAAACCTCACCTCAGTGTGGGAGCGGAGGGCACGCCTGCCCCAGGGACTCCTCCCCTCACAATCACCAAGGCCAGGCCCTCGAAGCCTGCGTCTCTCGCAATCCCAGCCCACTCCTGTCACCCAGGCAGGGCACCCTGTGGCCTGGCCAAATTAAGGGTGGGGCCTCTCCATGGGTGCTCCCTGGGTGGCTGGGCCTGGCTGGGACATCAGCAAGTATTATTTGGAAAAAAAAGCAATTTATTACCTAAATCACAGAAGCAGTCATTAGAGAAGATACACCCCTATTTGTAGGATTCTACTGGACTTAGTTCCTCCGAAATTGGTGATGTTTTAGTTCCTAATGCTGGCACCCAGCGGCTCTGGCCCAGTGGCCTTCATGGCTCCAGCTGTGGGGTGTGAGGGACTGGCCCCAGATGGGTCCTCTCCCTCCGGATTCACCTTCCCAGATCCAGCATGGGTCCTGCAGGCAATGGCGGCTGGGCTCCCCGAGGTCTTTCTGAGATTGAGGTTCCCTTCTCAGTGGGAGTGGGCAGCTCTGCCCCGGCGGCCAGGCTGGCGACCACCCTGCAGGGCCGGACAGAGCCTTCCTCCGGGGCCGCCTTCCCAGGCAGCCGCTTGCCTCTCTCCAACCCGCTCGGGGCGAAATGAGCCTCGCGCTTCCGCGCTGAGCCCGGCCCTGTGCGTCCCGCAG
Seq C2 exon
GCGCTTCGGGACCAAGTGCGCCGCGTGCCAGCTGGGCATCCCGCCCACGCAGGTGGTGCGCCGCGCCCAGGACTTCGTGTACCACCTGCACTGCTTTGCCTGCGTCGTGTGCAAGCGGCAGCTGGCCACGGGCGACGAGTTCTACCTCATGGAGGACAGCCGGCTCGTGTGCAAGGCGGACTACGAAACCGCCAAGCAGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107187:ENST00000371748:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.014
Domain overlap (PFAM):
C1:
PF0041217=LIM=PU(94.6=91.4)
A:
NA
C2:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACATCCTGGACCGCTTCATC
R:
CTGCTTGGCGGTTTCGTAGTC
Band lengths:
342-1043
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains