HsaINT1018199 @ hg38
Intron Retention
Gene
ENSG00000107187 | LHX3
Description
LIM homeobox 3 [Source:HGNC Symbol;Acc:HGNC:6595]
Coordinates
chr9:136198908-136199880:-
Coord C1 exon
chr9:136199678-136199880
Coord A exon
chr9:136199060-136199677
Coord C2 exon
chr9:136198908-136199059
Length
618 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGC
5' ss Score
5.66
3' ss Seq
ACCGCTCGCCCGCCGCGCAGAGG
3' ss Score
6.35
Exon sequences
Seq C1 exon
GCGCTTCGGGACCAAGTGCGCCGCGTGCCAGCTGGGCATCCCGCCCACGCAGGTGGTGCGCCGCGCCCAGGACTTCGTGTACCACCTGCACTGCTTTGCCTGCGTCGTGTGCAAGCGGCAGCTGGCCACGGGCGACGAGTTCTACCTCATGGAGGACAGCCGGCTCGTGTGCAAGGCGGACTACGAAACCGCCAAGCAGCGAG
Seq A exon
GTCAGCCGAGGGGACGACGCTCCCACCTTTCCTGGTCTGAAAAAAATGGGGCTGAGGCCACGCCCAGGGGGGCGTCCGGGGAAATTCTCTCCCCAAGCGCTCACTAAGGGGGCCTGGGCTAGGGCGGTGTAGGCAGCAGGAAGCCGAGGCCGGGAACGGCGGAGTCACGGACAGACCCGCGTCCCGAACCGCTTCGTTCGGTCCGAAGTGTGCGGCTTTTCGCCCCTGGTCGGAATTATCGCCCTAAATTCTTGGCCGCGAAGGCTGGGCCATACCCACACCCTTAGAATAAAGGGGAGCCCGCGGGGAAATCAGGGTGCTTGGAGAAGGGAGCCAAGGCTGAAGGCGGGGGCGCCGTGGAGGTGCGATTTTAGGGAAGGCGCCGCCCCCGCCCCCGCGGCAGAACCCGCCCTCCGCCGGCGCCCCCTCCACCCCAGCCCGGGTGCTGCCCGTTTTTGCCAATCGCTCCCAGCGCCCGCGCCTTCCGAGAAGCCTGTGGGGCGGGATGGGGGTGGGCACCTGAGGCCCCGACGTCCCCGCGCCGGCCGGGGTGGGAGGGCTGGGGGTCCGGCCGGGGCCGGAGGGGCTGCCGCGCCTCACCGCTCGCCCGCCGCGCAG
Seq C2 exon
AGGCCGAGGCCACGGCCAAGCGGCCGCGCACGACCATCACCGCCAAGCAGCTGGAGACGCTGAAGAGCGCTTACAACACCTCGCCCAAGCCGGCGCGCCACGTGCGCGAGCAGCTCTCGTCCGAGACGGGCCTGGACATGCGCGTGGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107187:ENST00000371748:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.706
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
A:
NA
C2:
PF0004624=Homeobox=PU(77.2=86.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGCTTCGGGACCAAGTG
R:
ATGTCCAGGCCCGTCTCG
Band lengths:
342-960
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains